I also ran into this problem just now -
I had a single repository with a child XLink.
I was moving some files into/out of the xlink from the main project. But while I did that, I also moved a file from within the xlink to another folder in the xlink -- and deleted the origin directory of that file. In total there were only around 30 files being moved.
After reading this thread, I was able to successfully check in all but the problem file. That worked.
That left my "pending changes" workspace left with simply the moved file - and the deleted folder. I tried checking that in - and it worked fine.