I already came across one potential issue in general so maybe Szsori knows a good way to avoid this or a solution.
Xfactor is the example I found. I am guessing during the upload, the zap2it ID was added to the British version. The US version is as a result missing the ID#. S
http://www.thetvdb.com/?tab=series&id=230121 - X Factor (US)
http://www.thetvdb.com/?tab=series&id=74626&lid=7 - X Factor
It looks like the merge is doing this for any show where the basic version isn't the US version. The same thing happened with Hairy Bikers.
The same thing appears to be happening with the series with a year. For example Castle
http://www.thetvdb.com/?tab=series&id=82607&lid=7 has the series ID of Castle 2009
http://www.thetvdb.com/?tab=series&id=83462&lid=7.