It seems I found a solution...
Right after I wrote that I haven't changed anything in the way I convert books, I remembered that some time ago I enabled sharing content via FB in Calibre. Today I made an experiment and ticked this option off and then converted those troublesome books and sideloaded them again. And it works! Although I don't know how
But the books disappeared from the homepage after I added them to collections, and everything works fine now
Anyway, thank you for replies