Ugrade Qubes 4.0 to 4.1 - qrexec_timeout errors @ Stage 1

I am trying to upgrade Qubes 4.0 to 4.1 (using qubes-dist-upgrade) but the process fails at stage 1 because the virtual machines are failing to start within 60 seconds. These virtual machines qrexec_timeout values have been set to reliable values (using qvm-prefs) but it appears these values are ignored by the upgrade process.

Is there a configuration file or etc. for qubes-dist-upgrade where the default qrexec_timeout value can be configured in order to work around / fix this issue?

This may be a bug. Please check

You are doing an in-place upgrade. There is another way to update which may work. Check that here:

As far as I know I am following the only method provided for upgrading i.e.

Yes. Exactly. If that method is proving too troublesome, you can do the other method.