Hello,
Ah, this could be issue with old naming rules. If they are left in project directory they will be ignored when deleting, updating etc...Also, if file's are write protected this could cause a problem but that you should be able to see an error in a log.
You could use "Save Project As..." to save it on different place and get rid of garbage you have or remove wrong files in file system manually(just delete them). So, make a backup( just in case ), remove duplicate test cases and do save as...
If you still have problems, let me know, so we can fix them asap.
robert