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73416ba
(Get the code!)
Also affected, although nothing to do with a multi-gpu system. Mint 17.3 (64-bit, Cinnamon) and a local /etc/X11/xorg.conf to slow down my crazy-fast Logitech mouse. Installing fglrx renamed xorg.conf to xorg.conf-DATE (and put nothing in its place).
Not a huge problem in this case, but certainly rather uncourteous of it. If this is an involved problem, perhaps at least this specific situation could be worked around by not moving xorg.conf out of the way if it isn't being replaced by anything. That is, I imagine it could be generally troublesome to merge a local configuration, but merging with a new /empty/ configuration is not. If a new xorg.conf is in fact generated, maybe a user warning if an old one was also found...