It is for this exact reason that I have a custom column called "Original Filename". So I can always replace the original copy on my Kindle Touch cleanly, preserving annotations and pagenumbers.
I would be even happier if reading metadata from filename would fall back on reading from the file contents for metadata fields not named in the regex. That way, I could have the filename automatically imported. Even so, as part of my obsessive cleanup and normalizing routine, it doesn't take long. Small chunks at a time is the key to metadata control.
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