Is there a way to prevent a file in system/media from being overwriten by a ROM flash

There is a bug on Android since 2.2 that make apps "forget" notification sounds from SDcard after rebooting or unmounting it. The solution for this is to save those notification sounds on the system/media/audio/notifications folder.
The problem is that I'm running CM10.1 Nightlies and each update reflashes the notifications folder, erasing my notification sounds.
So my question is: is there a way to prevent this without having to modify the zip file itself?

Thanks in advance.
--
Sent from my Samsung Galaxy S Captivate using My Hands™ (and probably Tapatalk)

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