There's a confusion here - qrexec-timeout is the time to wait on boot
for the qrexec agent to be connected.
If the qube isn't booting up then you have no chance of performing an
upgrade. You should fix that problem first. BUT...
The fact that "the VM is forcibly stopped after 15 minutes" suggests to
me that you have the idleness monitor enabled, since this *does* have a
default shutdown time of 15 mins.
Can you check to see if you have the shutdown-idle service enabled this
qube?