I discovered independently yesterday that I have the same problems created by choosing merge citations. However I think that my last known good backup is from last October when I first switched to RM8 from RM7. This means that I will have to redo hours and hours of work … and yes I do backup every time I use RM8 but a backup of bad data does no good at all 
I have found the problem in many many sources and I think it is a bit disingenuous to blame the problem on how Ancestry might handle sources and citations.
As a user (even as a user with years of professional IT and computer experience) I would assume that when a program says it will merge identical citations that it would do just that. I would never for a moment think that two citations with different media attached would be considered identical citations.
Now that I am faced with a monumental cleanup task I may just also try out competing genealogy programs after being a faithful RM7 user and RM8 tester. The various “problems” in RM8 usability such as multiple mouse clicks for simple tasks compared to RM7 combined with this merging citations idiocy have, I think, brought me to the end of the road with RM8.