Yes, it would become messed up. In fact, that's exactly how I found out about the problem.
Load the *free* comic book reader app CloudReaders, transfer a ZIP, RAR or PDF file containing your comic book to the app via iTunes, and enjoy! The app will remember the last page read in all of your comic books, and includes a toggle button to reverse the page flip order for the books that must be read right to left.
GoodReader is another option, but you have to pay for that one, although I believe it's only 99 cents. However, I don't know if it includes any DRM protection schemes. On top of being a cheapskate, my personal preference is to avoid DRM altogether because of its all too frequent tendency to screw up even on your legitimate purchases.