OK, I checked. Calibre did almost nothing to the epubs I downloaded and added to the Calibre library and then sent to my device from there (a KOBO Libra H2O).

OK, I checked. Calibre did almost nothing to the epubs I downloaded and added to the Calibre library and then sent to my device from there (a KOBO Libra H2O). The only thing it did was to add a file `./META-INF/calibre_bookmarks.txt` to the zip archive. The HTML was completely untouched. Now obviously if you do some conversion it's going to be another mattter and it's possible that the Calibre checks for some things it considers incompatible with its reader and in those cases alters the HTML, but I didn't find anything like that in the books I checked. Admittedly I don't think that Calibre should touch the contents of an ebook zip file without specific action from the user (such as requesting a conversion)... but what it does doesn't seem to be problematic.