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I just tested this:
Picked a book and viewed it to confirm that the metadata in the book (ePub) is consistent with the metadata in the DB (I'm using the Calibre ebook viewer to read in-file metadata via the "i" button). Edited metadata and re-viewed the ePub, the data is the old metadata (this is, as I wrote expected behaviour). Converted to Mobi (I didn't want to overwrite my ePub) and viewed the Mobi file, the metadata is the edited metadata (Again, this is expected behaviour).
The file names would of course change, since Calibre needs to keep the library folder structure in sync with its database. I forgot to monitor that during the test, but a quick metadata edit confirms this.
I'm not totally clear on what behaviour you're seeing, in your last post you mentioned seeing no sign of the old metadata in the ePub file, implying that Calibre updated the in-file metadata during your edit? Also, the metadata in metadata.opf is kept current the same way the file name is kept current.
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