No. CVS *never* removes a file that it doesn't own. What should happen
in that case is that CVS should checkout the files into the existing
directory tree, complaining about any existing file with the same name
as one it is trying to checkout (and skipping the checkout for that
file). In reality, CVS doesn't work very well in this case (and exactly
what it does is almost certainly different depending on whether you're
using client/server mode or not). It has a tendency to refuse to
recurse into existing subdirectories at all, and you may get additional
errors. But it will never remove or replace an existing directory or
file.