I was having a conflict where the S+ (Structures Plus) would overwrite vanilla engrams required by the CKFR mod. Specifically the Wooden Fence Supports.

I dug around and figured it out we need to add this command to the GameUserSettings INI. It will prevent S+ from overriding the vanilla engrams, so you can still have both. I included the Fence Foundation too just to be safe. You also need to include the Wooden Foundation and Thatch Foundation since those are prerequisites and get replaced. I'm sure there is a way to remove all prerequisites too to make it easier though...

[StructuresPlus]
EngramOverrideBlacklist=EngramEntry_ThatchFloor_C,EngramEntry_WoodFloor_C,EngramEntry_FenceSupport_Wood_C,EngramEntry_WoodFenceFoundation_C

-edit-

I just noticed a main sticky post on the S+ mod page that deals with all this too. They suggest more to add as well.
https://psteamcommunity.yuanyoumao.com/workshop/filedetails/discussion/731604991/4203492762828911242/