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Along those lines, you could probably convert the RTF to epub, and if it really is missing formatting present in the epub you have, after converting, you could use diff to extract the differences including the formatting, and then edit the diff to remove the other changes.
Then if newer rtf's come out, you can reconvert them and reapply the formatting changes.
Quite possibly, you could even leverage the tools in git to do some of this automatically.
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