When I first joined this forum over three years ago or so there was always a lot of posts about their arduino boards not able to upload sketches any longer. In lots of cases reburning the bootloader got them functional again. But there never seemed to be any progress on identifying what the root cause (or causes) of this kind of failure was. At the time I offered up a question of sort to the software gurus to see if anyone could create a sketch in the IDE that could be complied and uploaded to a board which then resulted in not being able to upload any other sketch again to the board. I don't believe anyone came up with an example but that's not saying it's impossible I guess, as I said many have recovered from there fault whatever the cause by just reburning the bootloader. Burning a bootloader does result in having the fuses set to proper values as well as the bootloader code installed.
So while the problem symptom dates back for a long time, I don't know if we have ever identified the source or reasons for bootloader code or fuse values being corrupted once loaded correctly.
Lefty