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This is generally a reference to Calibre.

If you have a document which does not any extra code in it, running it through Calibre will cause it to pick up what some consider extra unnecessary code. This is because Calibre does things in a certain way that produces workable code from almost anything and from nearly any source.

If a document is unusable in an e-reader because of errors, sometimes converting from epub to epub will clean up those errors and create a useable document.

If you have ever spent time trying to fix what seems unfixable, this can be a godsend.

It is evil only to the extent that Calibre may turn what some consider to be a sleek sports car of a document to much less elegant, but highly useful family car. Really more a matter of taste, as both can work, but a calibre product can be a probably unmeasurable bit slower and harder to understand for someone who wants to fine tune it.