Here's a repro:

$ mkdir -p ro rw union ro/dir
$ unionfs -o cow rw=RW:ro=RO union
$ touch ro/dir/{f1,f2,f3}
$ cd union
$ ls dir
f1
f2
f3
$ echo hello >dir/f2
$ mv dir otherdir
$ ls otherdir
f2
$ cd ..
$ fusermount -u union

The second ls doesn't show f1 and f3, only f2 that I have modified. The most annoying thing is that this happens completely silently, one has to be lucky to notice such file disappearance. Not sure I understand how complicated the problem is, but I'd be happy if such a rename would just error out rather than work erroneously. :(

I've checked previous issues (#23, #25, #27) but I couldn't really tell if it's the same problem or not so I thought I create a separate issue for this.