Yes I know all of the above and still they disappeared after a brief flash. I've sold the problem now by rebooting; it seems I need to reboot before everything. Time to backup and fast.

I've been using AOMEI but it's slow and I'm not sure if it makes a bootable copy (never had to find out). Is there anything better? At least there were no errors detected on the HD according to SFC so it might just be the HD that's wonky.