You sir are having the same problem me and sin were having until we started making some progress. It’s with the Referencing, if that’s not done right it won’t cook right. As well as the naming (for some weird reason).
For me I just renamed my PrimalGameData_BP_Generic mod to GenericMod_PrimalGameData_BP and made sure it referenced all the other Blueprints/classes I needed and everything seemed to cook fine. But for sin it worked once and then started giving trouble again until he was able to figure out his solution.
Sadly creating mods is harder than it should be since cooking is very tricky.