Most patches for SK used the previous menu structure. Because I have completely restructured the menus in SKE older SK patches may not be compatible. Only patches that alter the section Constructible Objects are compatible with SKE. When you open a patch in FO4Edit, if you only see a Constructible Object section as shown above, the patch should be safe to use. Until mod authors start updating mods specifically for SKE, older SK compatible patches will not use the new categories I have created. The Constructible Objects are the recipes you use to craft something from the settlement menu. Changing those makes the item appear in the appropriate menu. As shown above even if you see a lot of red that is still okay. It's red because Keywords are flagged in FO4Edit as important changes.
When patches alter the section FormID List those interfere with the DLC menus and the new menu layout in SKE. In the example above, the numbers that start with [00]-106DA3 mean it's altering records from Fallout4.esm. When mods alter records from Fallout.esm or SKE those patches will cause conflicts and menus will no longer show up in game.
When patches do not alter records from Fallout4.esm or SKE there will be no conflicts shown. The example mod above only adds new records in the mod. Patches that don't alter records from Fallout4.esm or SKE, may still be usable but you will need to test and examine them further.