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The convertible top really shouldn't affect the the rear panel, it's not in direct contact with the roof mechanism. Just make sure you get it repaired at a BMW recommended/approved/authorized repair shop and it should hold up. A good shop will back it up with a warranty as well.
If you're no satisfied with that, then you can try to get them to replace the whole panel instead of just repairing it.
Edit: Or you can get it fixed and sell it to some other smuck (with full disclosure of course) and get yourself a new one!
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