I've got another vote for an "it depends".
I have PRC (Mobipocket) and PDB (eReader) ebooks that I liberated with earlier versions of the scripts that I was happy to read as-was, but newer versions of the scripts have left more true to the original (for example, I noticed recently that none of the italics had converted on one pair of ebooks I converted three years ago but only now got around to reading).
So having the original means I can run the newer scripts and have nicer copies of the converted.
Also, I have ebook versions that have the newest Calibre "title page", the previous version, and none. I have ebooks that I hard-coded as 12pt, then 14pt, then 16pt font (as my vision goes - jeez, it sucks to get old!)
For some of them, I've had better results using the original file and basically starting over. Some have "upconverted" okay from my initial set of Calibre files.
All that makes it useful to me to keep my original files. Besides, if somebody really starts fussing at users who liberate books for their own use, I can at least prove that I bought the original copy!
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