This is curious.
Last night I updated my Win10 tech preview to the latest build - oh boy did that cause a headache in the end. On Win10 side everything was fine, but somehow updating it to new built messed up my Win8.1 installation which resides on completely different hard drive and they're not aware of each other via boot manager or such either.
When I came back to Win 8.1, CCC thought I don't have AMD graphics card anymore, reinstalling and uninstalling drivers didn't work (several errors about temp folders and what not). Also Windows thought both my monitor and TV are my TV. Removing the video card from device manager didn't help either, still couldn't install drivers for it.
Few reboots later, Windows decided to run some "disk repair" thing on a drive that neither Win10 nor Win 8.1 is installed on. Still, after it, nothing really changed.
Then I ran sfc /scannow, during which (probably not related to running it but still it happened during) my screens blinked and suddenly I had the previously removed Catalyst Omega's installed again, CCC worked fine too, and so did everything else by the looks of it.
sfc did find some errors and now my machine is telling me to reboot to fix drive errors but I'm afraid to
And no, the hard drives don't seem to be broken, they go through all the tests with flying colours.