Because of the different types of files that are available, which in turn must interact...

You have definitions for Colorschemes, Aircraft Variants, EA's ( entire aircraft), etc.

Normally the plane installer will warn you and prevent the installation of colorschemes and variants that you do not have the base aircraft for. However given the rather random naming used by people creating their own aircraft. the program can be fooled.

If you then in turn go and try to remove the files, and miss one, or do not remove the entry in Realflight.ini, you may continue to receive the error.

After all files are removed ( which you've obviously done correctly ) the realflight.ini entry can still remain behind until the next time the user created respository is rescanned. That may happen when you add a plane, variant, or colorscheme later. The entries in the .INI file are rebuilt.

The end effect is exactly what you've seen, the error appears to go away by itself.