If you can, install Debian on a completely fresh disk (may be a good idea if you used your old one for a few years), so that you can mount your old Windows drive in Linux and copy files as needed. Once you can work for a few weeks without missing anything critical, you can then nuke your old drive.
Krita stores various config files in User folder in AppData Local and Roaming. You would need to copy the config and resource files from there. I’m not sure, but I believe they are largely platform-independent.