Plan on the task taking a LONG time. I recently removed 20-30 projects from GrabCAD's servers. When deleting large numbers of files, the command would work quickly or the page/site would sometimes hang on the deletion confirmation dialog box. After a while, the "delete" button would turn red again and the files would not get removed.
The problem appears to be worse with large file sizes, each of which may have hundreds of versions. I was able to remove the bulk of the files quickly but the last 1000 have taken 10 days or more. I have 2 files left now. It is painful.