For this reason, we suggest you use GNU patch when applying patches. This step will only patch the differences in existing files. Do a 'diff' to discover any new files or directories. Pay close attention to the output of the diff. You want to make sure you don't accidentally include garbage in the new release, or leave left-over files which will conflict with changes in the next release.
Directories are a little trickier to remove.
The reason they are so hard to remove is because CVS isn't built to handle them yet. The preferred hack is to just exclude the directory from the module checkout line. Otherwise CVS commit will barf and you'll have to start all over again. Wipe out the newrelease directory and begin at step 1. As long as you don't commit you won't mangle the release.