Do this:
Step 0: Backup the current non-working VM. It is always good to have backups. Even if it is partially-working.
Step 1: See if Volume backup and revert guide works.
Step 2: If the above (or increasing qrexec_timeout) does not work, you could use qvm-block to attach the private volume of the appvm to another working appvm. There are many similar Q&A on forum. Such as this one. Read few of them and follow their guides.