I think there are some leftover or junk files called redirects in folder of unreal project. Those tend to mess everything in.
I tend to close finished (or just matured) blueprints into macros, comment them well then save as macro library.
If anything gets corrupted i can copy macros from backup and recreate easily.
However once i messed whole folder structure to the point that i recreated whole project, but with macros copied over.
And yes blueprints are not meant for huge games, they are fast tool to make small things. Use them for what they are made for.
Epic showing off they can do games, is just makreting, there is reason they use C++ for Fortnite instead of pure blueprints.