hey, I had same issue.
the problem was that couple of assets and C++ classes were referencing animation blueprint with those functions. In C++ classes constructors contained ConstructorHelpers::FObjectFinder and hard coded references. Also some widgets were to blame. And since those finders were in constructors they were called during CDO creation phase, which is somewhat earlier than plugins are loaded.
So general idea is to break dependencies on ABP_Item_LayersBase.
for example do not link that ABP directly to main ABP instead do it in Player controller on Possesion. Use interfaces instead of direct casts to main ABP.
Also you could set breakpoint in LinkerLoad.cpp:3267 then go up the call stack to the first Verify call and look what path inside of this pointer and get all of problematic files right away