We disabled tagging for the RDz "RemoteSystemTempFiles" directory because we were tagging duplicate copies of files, both in that directory and other places. Duplicate symbol definitions were populating the workspace tag files. But apparently, you are saying that some (all?) of these mainframe files are only mapped to be under this directory on the local drive? This is different from what was being reported to us...working within "other" Eclipse-based products is always challenging...sorry for the trouble.
At any rate, attached is a hotfixed version of maketags.e and maketags.ex. Backup the existing copies you have of these files at ECLIPSEDIR/plugins/com.slickedit.windows.libs_3.6.1/slickedit/macros/, and save the attached versions to this same directory. Now go to Tools > Retag Workspace. Everything should be tagged...let me know. This isn't really a general purpose hotfix, because I'd still like to know more about what is going on...but it should prevent any workspace directories from being excluded from tagging.
If you feel like elaborating more on how your RDz workspace is set up to work with the remote mainframe files and local directories, that would be much appreciated as well.
- Ryan