This exact problem happened to me recently in Qubes 4. The steps outlined here worked.
The commands for me were along the lines of: sudo xl console, pkill -u 1000, umount, e2fsck, resize2fs.
A HUGE THANK YOU FOR DOCUMENTING ALL OF THIS HERE! Excuse the yelling, this is my excitement about having this resolved 
Additional note: Since I had snapd installed in the TemplateVM I needed to remove this too to get rid of its mounted file systems in the AppVM.