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If you aren't using the OTA function and download the updates off the OTA server(s) using your PC, you can control the merging process and not change what you don't want changed. (At least for your Kobo, I am not sure if that would be the same for the Kindle)
If the OTA process uses a merge procedure that only replaces files of the same name and adds only new files, your "myepub.css" or "user.css), if you prefer, should be there after the OTA update, as well.
Luck;
Ken
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