Rob,
Here's what R&D had to say:
"First run SCC >> Project to delete the files from the local dir. Then run SCC >> Advanced, from this dialog select Show All Files from the pull down list. Use ctrl-click to select all the files in the desired project, then click on Delete. This will delete all the files in the project from SCC. Note, after this operation a number of empty directories may be left on the master (where the project used to reside), it should be safe to delete these dirs."
I hope this suggestion from R&D helps. Thanks for your patience on this, and have a pleasant day.
Sincerely,
Darren Nattinger
Applications Engineer
National Instruments