It's me again, working at resolving potential conflicts with Cities of the North - Winterhold. Each mod which has a patch is listed below, with specific details of all changes contained in spoilers, if necessary. All patches are ESP flagged as ESL, unless otherwise noted. I'm certainly more experienced than before, but I'm always learning, so if you run into trouble, please let me know and we'll see if we can work it out.

Please remember that patches sometimes involve Persistent references, so they will require a new save/playthrough. Before making a request for help, please double check that the problem exists on such a new save.

Included Patch Descriptions

3DNPCs/Interesting NPCs - shifts placed objects/markers to match new interiors. Last checked against version 4.4

AI Overhaul SSE- shifts some placed idle markers to match the new interior/exteriors. One package conflict resolution. Last checked against version 1.6.6

Amulets of Skyrim - Moves three amulets to their appropriate locations in the new interiors. Last checked against version 4.061

Animated Armoury - DAR Edition - Moves two books to match the new interior. Last checked against version 2.3

Artifacts of Skyrim - Revised Edition - Shifts a placed object to match the new interiors. Last checked against version 1.0.1

Atlas Map Markers - NOTE: Based off MCM version. Shifts map marker for Birna's Oddments to match new layout, adds map marker for Stonecold Fortress. MCM toggles supported. AMM patches are being released for other patch collections shortly, and will require end-user CR between patches in order for MCM toggling to work for everything. Last checked against version 2.0

BadGremlin's Collection AIO - Moves a placed fish to its appropriate location in the new interior. Note: Patch is for AIO, not for the Fishys .esp. Last checked against version SE1

Cathedral - 3D Mountain Flowers - CR for new snowy flowers type. Last checked against version 1.8

Cheesemod for EVERYONE - Shifts a few added cheeses to match the new interior. Last checked against version 1.0

Complete Alchemy and Cooking Overhaul - Reposition of new vegetables added by CACO. Last checked against 2.0.8

Cloaks of Skyrim - Moves two placed cloaks to appropriate locations in the new interiors. Last checked against version 1.2.1

Curse of Akavir - Phoe - Shifts one NPC to match new interior

Enhanced Lights and FX - One patch for simplicity's sake this time. Patch attempts to replicate the intention behind ELFX to the new interiors, however, due to engine limitations a few compromises were made. I'm looking for feedback on this one, for any interested. No changes made to the newly-added cell. If using ELFX Fixes, load after ELFX Fixes. Last checked against version 3.06.

ELFX Exteriors - Patch for outdoor lights which are added by ELFX Exteriors. Last checked against version 3.06.

Embers HD - Conflict resolution patch for the Inn. Last checked against version 1.4.

Embers XD - Shifts the placement of fires to better utilize the new look of Embers XD, includes some ashes spread around, and in a few places substitutes
fire types to better match aesthetics. Last checked against version 2.4beta. Won't work with versions prior to this.

The Great Cities - Minor Cities and Towns - Reverts all changes made by TGC. Forwards COTN with any conflicts. Effectively disables TGC's changes for Winterhold, allowing COTN to be used. Any TGC patches will need to be handled by the end user. New game is absolutely, 100% required. Last checked against version 2.01. An alternative patch can be found over here by Adrien2401 which keeps TGC Winterhold layout, but changes the Jarl's Keep to use COTN Winterhold's

Guards Armor Replacer - Shifts placed armor to match new interior. Last checked against version 5.5a.

Harvestable Mammoth Skulls - CR for conflicts, changes all added skulls (even ones that can't be reached) in the Jarl's keep to be harvestable. Thanks to Pippa for the patch. Last checked against version 1.0.

Immersive Citizens - AI Overhaul - Forwards COTN changes to bed and chest in Birna's Oddments; Shifts new markers to match new interior in Frozen Hearth, restores the bed pointed to by ICAIO package and replaces the newly-added bed with it; Shifts new markers in Jarl's keep to match new interior (including shifting one to upstairs), restores two beds pointed to by ICAIO packages and shifts them to the new upstairs cell to replace newly-added beds; Updates COTN Winterhold AI package to point back to the original bed; Updates ownership of the upstairs cell to match the new ICAIO group. Last checked against version 0.4

Immersive College of Winterhold - Shifts scrying location to (hopefully) cover the new interior. Last checked against version 6.2

Immersive Wenches - moves a bunch of markers to match the new interiors inside The Frozen Hearth and the Stonecold Fortress (fancy new name!). Edited packages to match new stuff. Last checked against version 1.60SE

Large Trees - Resizes 6 trees from Skyrim.esm which clip through the bridge when using a mod which increases tree size. No master set, so
should work with any mod that increases tree size. Thanks to Deigue for the patch. Alternative version by altonjarrod is designed to work with Simply Bigger Trees, as well.

Landscape and Water Fixes - Forwards COTN Winterhold changes wherever appropriate, forwards ownership of the chicken nest from Landscape and Water Fixes. JKs, non-JKs, and JKs+MLOS versions available. Last checked against version 6.3

Lanterns of Skyrim II - Shifts lanterns to match new exteriors. Shifts a few lights and such, too, resolving conflicts. Adds a couple braziers simply because I thought it looked nice. Adds a few more light sources in appropriate spots. Choose only one of JKs and non-JKs version. Shifts some wind blowing FX to match new exteriors. Last checked against version 4

Legacy of the Dragonborn - Moves a few fliers, drunk marker, Latoria, restores one bench used by a package, and a few items in Birna's Oddments. Last checked against version 5.5.2.

The Midden Expanded - Shifts a few things in the interior of The Frozen Hearth to match new interior. Last checked against version 1.07. Patch provided by SeaSparrow. Lite version available here

Midwood Isle - Shifts the location of some of the worshippers, an auto-load door and a marker, and a chest to match the new interior. This is quest related so it hasn't been fully tested yet, and as everything but a quest stage trigger are persistent objects, will require a new save. Last checked against version 2.7

Morrowloot Miscellania - Item Distribution - moves one placed book to match the new interior. Last checked against version 1.3.

Morrowloot Ultimate - same changes as Morrowloot Miscellania - Item Distribution. Last checked against version 1.54.

Mystic Condenser - Fixes placement of the Mystic Condenser put in Stonecold Fortress. Last checked against version 2.3

Nchuanthumz - Creation Club patch. Shifts a note inside the Windpeak Inn.

No Snow Under the Roof - Forwards COTN Winterhold to win all conflicts, disables any added references from NSUTR except the sign. JKs patch is included for conflict resolution against the general JKs patch, applying fixes to the COTN - JK items that are added. JKs patch has non-JKs as a master. Thanks to Deigue for the JKs patch. Last checked against version 3.2

Notice Board - Shifts the notice board to match the new inn exterior. Thanks to EiraSvero for the patch. Last checked against version 1.4

Off Limits - shifts, resizes and adds trigger boxes to match the new interiors layouts. Last checked against version 1.2

Open Civil War - Consider this one a beta. There are two markers (for attack/defense) which previously were put over the Jarl's door as you exited the building. However, now the keep is way up at the top of the hill - I have moved this marker down to where the path ends, so it's close to town again. I presume going into this trigger is what starts the attack/defense (so you won't be way off away from the action at the top of the hill), but have not confirmed it. Please let me know if you run into any problems. Last checked against version 2.6.3.

Populated Skyrim HELL Edition - shifts markers to match the new interiors/exteriors. Last checked against version 4.1.

Populated Cities and Towns - shifts markers to match the new interiors/exteriors. Last checked against version 4.1.

Snazzy Furniture and Clutter Overhaul - Shifts placed paintings to match new interiors and updates furniture to match theming. Last checked against version 2.0

Skyrim Artwork Imports - moves any needed objects placed to match the new interior. Last checked against version 1.0

Skyrim Underground - ties the trapdoor in The Frozen Hearth's basement into the new navmesh. Last checked against version 4.6.1

Skyrim's Unique Drinks - Shifts drink placement to match interiors. Last checked against version 1.0

Skyrims Unique Treasures - Shifts placed objects to match new interior. Last checked against version 4.4

Sounds of Skyrim Complete SE - for tonycubed2's version of the mod. Shifts the position of some sound
markers, adds a few new ones, and forwards acoustic space changes. Last
checked against version 2.0.

Thieves Guild Requirements - Shifts placed marker to match new interior. Explicitly for version 5+

Thieves Night on the Town - Shifts placed objects to match new interiors. Last checked against version 1.0.2

Training Dummies Provide XP - CR, applies changes to newly added dummies. Last checked against 1.1.i-guess.cant-remember-tbh

DX Ursine Armor Pack - Shifts the crafting book to match the new interior. Last checked against version 2.0


Other patches that I'm aware of: Distinct Interiors, Immersive Laundry, Keep it Clean, Outlaws Refuges, Winterhold Keep Tweaks, The Midden Expanded, Skyrim Unbound Reborn

Installation
Use a mod manager/organizer to install, or drop the loose files into your Skyrim data folder. Patches should have their appropriate masters set, and should be loaded after any mods which they are patching. Some of the fixes in question are on persistent objects, and may require a new save.

Compatibility
I don't believe this should introduce any incompatibilities beyond anything which may be present between base mods. Let me know if you hit anything.

Credits
Bethesda for Skyrim Special Edition and the Creation Kit
ElminsterAU for SSEEdit
JPSteel2 for Cities of the North - Winterhold
Kris Takahashi for Interesting NPCs and KaptainCnucklz for keeping track of it on Nexus
mnikjom and SpiderAkiraC for AI Overhaul
UNI00SL for Amulets of Skyrim
NickaNak for Animated Armoury - DAR Edition
HeiroftheSeptims for Artifacts of Skyrim - Revised Edition
Kronixx and kryptopyr for Atlas Map Markers
BadGremlin for BadGremlin's Collection
aviform, EpicCrab, DoubtSuspended, PhysicsFish, and Daniel Hodge for Cheesemod for EVERYONE
Nazenn for Cloaks of Skyrim
kryptoptyr for Complete Alchemy and Cooking Overhaul and Thieves Guild Requirements
Sengetsu for Curse of Akavir - Phoe
DeserterX for DX Ursine Armor Pack
mindflux for Embers HD and Embers XD
anamorfus for Enhanced Lights and FX and ELFX Exteriors
soldierofwar for The Great Cities - Minor Cities and Towns
NordwarUA and DanielUA for Guards Armor Replacer
woodtortoise for Harvestable Mammoth Skulls
Shurah for Immersive Citizens - AI Overhaul
Grantyboy050 for Immersive College of Winterhold
lordkoz for Immersive Wenches
jkrojmal and Teabag86 for JKs Skyrim
wizkid and lilebonymace for Landscape and Water Fixes
wizkid for Lanterns of Skyrim II and Tamriel Master Lights
icecreamassassin, SirJesto, and the LOTD team for Legacy of the Dragonborn and Skyrim's Unique Drinks
EasierRider for The Midden Expanded 
DdsLedg for Midwood Isle
foreverphoenix for Morrowloot Miscellania
ChocolateNoodle for Morrowloot Ultimate
Dave0523 for Mystic Condenser
prometheus for No Snow Under the Roof
mannygt for Notice Board
korodic for Off Limits
simtam for Open Civil War
the Sands of Time team for Populated Cities and Towns and Populated Skyrim HELL Edition
SenterPat for Skyrim Artwork Imports
clintmich and icecreamassassin for Skyrims Unique Treasures
AncientKane for Skyrim Underground
gutmaw for Snazzy Furniture and Clutter Overhaul
tonycubed2, Cliffworms, SirJesto and SOT Team for Sounds of Skyrim Complete
megapatato for Thieves Night on the Town
bmthrooh for Training Dummies XP