As many people with an iPad know, the PDF libraries included with it are written by Apple, not Adobe, and they don’t support all PDF feature perfectly. They’ve been working with freelance designers, myself included, to rid these PDFs of glitches (as much as you can when not always having access to the files used to create the book.)
I’m going to keep a running tally of which books I’ve updated using Tumblr: ipadrpgpdfs.tumblr.com/
Is this process removing features from these books when viewed on other devices or iPad/Phone/Pod PDF apps?
It shouldn’t, no.