If you have been previously using this mod's version 1 (or 1.0.1), you have to carefully read this guide:

Jaxonz Repositioner:

This is a mod that I encouraged people to use alongside this mod in version 1, however as of the new version, jaxonz repositioner, and other mods that move static objects, are all incompatible. The reason for this is that in new version the objects have embedded AI navigation information that these mods don't move. So if you move something from this mod using jaxonz repositioner, NPCs will think it's still where it was before. There is a spell available from merchant called “Move Shack Items”. Use this spell to move the objects from this mod as this spell has been scripted to move the embedded AI navigation information as well.

Disabling objects:

Since objects have AI navigation attached to them, you should refrain from using the “disable” console command on them, as NPCs will think it's still there. To destroy objects use the “Shack Destruction Axe” available from the carpenters.

Upgrading Toolset:

When you first upgrade to version 2 and run the game, you will be asked 2 questions. One asks you if you are upgrading from version1, and the next asks if you want the “CShacks Master Spell”. You should answer yes to both as these items are needed to make the things you have previously purchased and built compatible with the new version.

Kits:
Kits refer to objects that are either in your inventory or stored in some container. These reside in the misc category of the inventory, and are items that have not been built yet.

Changes:
If you're upgrading from version 1, these kits will completely stop functioning. Dropping them from your inventory will just make them disappear.

Fix:
You need to write down each object, and then drop them all (making them disappear). Once you have done that, use the Master Spell's “Get Item” feature to reacquire their new versions.

Important note regarding interior kits: (sheltered shacks, basements, and burrows) Your kit has an ID that is not visible to you. This ID will not matter if you have not built any of the same type of that interior dwelling before.
(Example, it wont matter if you have a full basement kit and you have built an empty basement before. The ID is only important if you have built an empty basement before, and want to build another empty basement again. Both “empty” and “basement”.)
If you have built the same type of the interior before, you have to avoid using the same ID twice as that will remove your previously built one. You can avoid this by saving the game and testing each kit to find your ID:
Move to your previously built dwelling. Use the Master Spell's “Get Item” feature to reacquire kits of that type one by one and build them one by one, until one of them removes the one you had built before in version 1. Remember the ID of the one that did and then load your save file and avoid using the kit with that ID.

Furniture:
These are your regular furniture such as crafting stations.

Changes:
These will work as they were before in version 2. However new items in version 2 have navigation information embedded in them so the NPCs can avoid bumping into them. Furthermore, the “Move Shack Items” spell and “Shack Destruction Axe” only work with furniture placed using version 2 kits.

Fix:
If you want the new features that come with version 2 furniture, first you need to delete them and then build new ones. To delete them open console and select the item, and then type “disable”, press enter and then type “MarkForDelete” and press enter again. (more info regarding console commands can be found in console commands section)
Once you deleted the previous furniture, use the Master Spell to acquire new ones and build them again.

Containers:
Chests, Barrels, End Tables, etc.

Changes:
Same as furniture.

Fix:
Same as furniture. However before you delete your v1 containers, use the “Container Transferor” from the Master Spell's console item section to move all the contents of your container to Master Spell's proxy container. (more info in “Master Spell Items” under “Shack Purchase Guide”). Once the old container is empty, you can safely delete it and make a new one as instructed for furniture items, and then transfer the contents back to the container.

Open Shacks:
Non-sheltered shacks.

Changes:
Same as furniture. The old ones will work, but if you want NPCs to correctly find their way around them you need to rebuild them.

Fix:
First get some chests using Master Spell's “Get Item” feature and place them somewhere nearby. Use the container transferor to move all of the shack container's contents to the chests.

When the game asked if you're upgrading from v1 and you answered yes, you would get an item called “Shack v1 Destruction Kit”. This kit should be used with extra caution: Destroying version2 shacks with this will leave the navigation info around and can cause issues. However in terms of upgrading, it allows you to quickly get rid of your old shacks without having to disable each shack prop one by one using console.

To use, stand in the middle of your shack and drop it from your inventory. Select yes and it will automatically destroy all shack props nearby. If some props were left, pick it up and then drop it again near them. Note that if your shack is built at a height, it may be advisable to use the “tcl” console command before dropping it to float and avoid falling to your death afterwards.

Once you have destroyed your old shack, use the master spell to acquire a new one, build it, and use the container transferor to move the contents of your container back into your shack. Finally, use the master spell to destroy the temporary containers you had built.

Sheltered Shacks:
Non-sheltered shacks.

Changes:
Same as open shacks.

Fix:
The interiors of the sheltered shacks have not been changed between the two versions, so you don’t need to move the contents of your containers like the open shacks.

To destroy, simply stand at the front door, and drop the “Shack v1 Destruction Kit” from your inventory WHILE SNEAKING. The kit will find your shack's ID and will put the corresponding kit in your inventory before destroying the shack. Once the shack's destroyed just use the kit that was automatically placed in your inventory to rebuild it. The interior will be as it was before and doesn’t need any updating.

Basements and Burrows:
The underground dwellings..

Changes:
Since the NPC can walk over these, the only new feature is the ability to destroy them.

Fix:
There is no need to update these. If you wanted to destroy your basement or burrow just use the console commands to disable the trap door. View the console commands section for more info.