Originally Posted by ocicat
The CVS tree contains branches which are no longer used...
True, but in this instance, the repeated warning message is referring to /cvs. This is usually the root of the repository. I think, in this case, either an incorrect cvs update command was executed, or (if used) $CVSROOT was incorrectly set. We haven't seen the commands used to produce the error, nor the $CVSROOT if set, so ... I wouldn't be able to confirm one or the other.
Odds favor the repository behaving correctly. Which means ... odds are long that there was a typo in either the -d option or the $CVSROOT if used.