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There are three types of problems I have seen from doing a conversion:
(1) User error - some setting in the conversion dialog makes changes to the ePub you did not intend to make, perhaps because they were your "defaults". A good example is splitting on h1/h2. In some books which use headings for other reasons it results in pages being split where you did not intend them to be. Or perhaps you have heuristics turned on and find the text content changed undesirably. Or you end up with double covers etc. Or perhaps you get an encoding issue which results in quotes being lost etc. You have to be very careful to make sure your "defaults" do not accidentally corrupt the book.
(2) Calibre conversion error - where despite your best efforts at disabling anything you can think of that might touch the ePub, Calibre insists on making changes anyway. An example I have hit several times is where despite having splitting turned off (the xpath set to '/') Calibre decides it will still go ahead and split some pages, in particular ones that contain images. This can be a problem when you have a title page and find it now gets split across multiple pages. The LOTR retail books are a good example of where this goes wrong that I hit yesterday.
(3) Internal structure changes. For a start the CSS gets "flattened" and considerable changes made to things like font sizes etc. Calibre also makes changes to the directory structure internally on the ePub. Calibre will also add attributes into the manifest and introduce other "foreign objects". For most users this stuff doesn't matter, but for some people it does, particularly those who use other tools with their ePubs.
Now provided you are careful, "most of the time" these things are not a problem if you are careful (or less picky about the result). However you should always inspect your ePub after a conversion to make sure it gives you the result you want. I cringe when I see people doing thousand+ book conversions - but that is because I have a very high level of quality I want in my books, to each their own.
The Modify ePub plugin is being developed as a halfway house between complete manual editing using Tweak ePub, and tasks that would normally require a conversion. It intentionally has limited scope of the changes it can "safely" make to an ePub, but it does not touch in any way the structure of the ePub or content outside of the specific options you check for it.
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