Pretty sure it wouldn't matter if a patch is applied, unless it was a patch that fixed an in-game glitch to your data, but then you'd be pretty well out of luck anyway.
I know you can just resume a game after a patch is applied, assuming you saved prior to patching, so a template should function the same as a save, with data saved upto that point.
The only thing a patch may affect as you are describing, is if you are playing live update, and a trade or something occurs in between your saving the template and current rosters, but I think you'd have this same issue from a normal save that way as well.
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