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Yuck. When I've had that happen at work, I've just did a hand merge. Let GIT tell you which ones it's having problems with. Then do a file compare and hand resolve the lines. It's a pain but better than having things get messed up. There probably is a better way to do it, bit I've never taken the time to learn or figure it out. Luckily I think I've only had it come up once.
I'm on vacation this coming week. So I can help if you need it with merging things.
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