Rematch is a Pet Battle Teams addon with a lot more features (auto team loading, levelling queue, search by ability/stats/etc.). It's a different interface than PBT, but I like it a lot better. The search feature is reason enough to have it even if you still use PBT for the teams. The other nice thing is the author of Rematch is still actively working on it. The PBT author hasn't done much since Nov 2013 unless he just came back or something.
It can also read the PBT file and try and make the teams. Not guaranteed though. If the file truly is hosed, then it will be really difficult to rebuild (have to by hand reading the file). Instead of the rebuild option, if you have PBT installed, go into the options menu of Rematch and look for an import button for PBT. It'll try to build them if it can.
The problem is older versions of PBT didn't save the teams correctly. They used the wrong ID for the pets (one that blizzard periodically changes). Newer versions of PBT and Rematch use a different ID to store the pets on the teams.
Here's the wowinterface link if you want to see if it can rebuild your teams for you:http://www.wowinterface.com/downloads/i ... match.html
It's on curse too.