Where did you upgrade it from? You sure you don’t have local SRP packages left in your directories in Assets or Packages? If you upgraded from 2018.1, you probably had something in local folders…
Ok… after a series of random Reimport All, the error remains, but after some more Reimport (not all) on certain folders it seems to trigger a sequence of “correct” dll rebuilt. Each time the error change places but eventually I got it all compiled without changes in manifest.
Really hope there is a “Reimport All Scripts” (without reimporting textures) that works, that is clean all the .dll residues that might cause this kind of problem. (Including packages dll, problem with incremental compiler, etc.)
Prefab overrides was not correctly migrated though (some previously not overridden field was overrided as null), but I can fix that manually anyways as I refactor things for nested prefabs.
Thanks for bringing this to our attention!
Could you please submit a bug report for this issue? A reproduction project would be great, too. It’s not possible to tell what’s going on from the info you’ve provided alone.