Productive Computing is pretty good at things and will probably have it fixed soon. But it is hard for third party companies to be ready for upgrades. But an altnerative might be the Solution Makes Inc. Quickbooks integration. Then again, I don't know if theirs works with QB 13 (b6). You might check their web page.
Update: We are calling it the 13-13-13 Easter Egg (or Rotten Egg)
version b6,June7. 6+7=13
Close everything down, open FileMaker with the actual date, and register the plugin.
Move the System date on your computer back by one week.
This should allow you to Synchronize. Note that you won't want to create any new transations, as they will have the wrong date.
FWIW, we have no problem with Productive Computing, We just don't want others to get stuck with same problem.
Looks like a brand sparkly new QB R7 update just became available, and it fixed one installation.
In the wider community of QB users, R7 is being blamed for introducing unrecoverable errors when external Apps make a Query Request to the Item List or an Add/Mod Request to the Employee List. I've read only one report that said R6 caused an Integrated Application problem that R7 fixed. The R6 update has been out for months, and while I saw several reports of instability within the native QB UI, I hadn't heard much about external Apps having problems with it. I watch the Productive Computing Support Forum pretty closely because I support a lot of clients with FMP/QB integrations, and there aren't any reports of R6 trouble there (but also none on R7 as of today, FWIW.)
Intuit has a "crucial fix" mechanism for rolling out vital updates, and it appears that they're using it to replace a bad file that was part of the R7 update. Once it's replaced, the problem is resolved. I'm guessing that your client's file was broken with the R7 upgrade, and then patched via the crucial fix mechanism. The bottom line for QB is the same as most software: don't rush to new versions unless you're having a problem that it will explicitly fix. Productive Computing may offer their own fix to this particular problem, but the fault in this case is almost certainly with Intuit.