Eclipse files out of sync autobiography

Occasionally
I get file out of sync errors, which I attribute the software I'm using
for synchronizing Eclipse with a backup server (after updating files on
the server, it sometimes needs to copy the update back to the Eclipse
directory to convince itself that the Eclipse version is not out of
date).

With source files this is harmless if annoying; I just open the
source file in the editor area, tell Eclipse the version is ok, and
we're back in sync. Today, though, Eclipse is griping about a .project
file being out of sync, and I can't figure out how to get it back in
sync.

I did a clean and rebuild on the project, and I tried changing a
proje