The title pretty much sums up the question.
I'm using windows 8.1 and ubuntu 12.04 in dualboot and now something in windows 8.1 broke and by the looks of it I may have to refresh/reinstall it.
Since I had to go through hell installing ubuntu (removing uefi boot, manually installing ubuntu then launching boot repair which created boot-grub for both ubuntu and windows) I can't figure out what will happen if I let windows 8.1 refresh/reinstall itself (windows 8.1 comes with a button for that and I may have to use it).
There are numerous questions about installing ubuntu alongside windows 8.1 but how to safely remove one or the other without having to throw your HDD?
If you reinstall windows it will make ubuntu not bootable. Ubuntu will still be there unless you repartition your drive, it just will not be accessible:
There is a section in this wiki that deals with installing windows after ubuntu. https://help.ubuntu.com/community/WindowsDualBoot