Hmm. That's odd.
Actually, that looks like it's a calibre bug with equality search by identifier.
I've opened a bug for it:
https://bugs.launchpad.net/calibre/+bug/1063395
I'd rather see it fixed in calibre than to try and work around it in FFDL.
In the mean time, you can still find and select the two books in calibre and hit update. Unlike add/update by URL, that will definitely update both correctly--there's no URL searching done in that case.
Jim