Deduplicating - unexpected over-ride behaviour
This does sound like a bug with 4.5.x. But it's worth noting that a lot of effort has gone in to improving the dedupe process in 4.7.x, and there are now automated tests in the core suite that test this sort of thing.

If you cannot recreate the issue on the demo sites (4.6.x LTS or 4.7.x) then I would say the issue has since been resolved and I would recommend updating to whichever version you feel more comfortable using.