Hi!
I just started to face a similar issue.
For the last 4 or 5 days, every time I reboot, all my PWA and Vanadium shortcuts are gone.
I tested various things and I could pinpoint the cause of the issue to a specific app. For some reason, if I create a shortcut to this Etherfields app (or to this one which as far as I can tell is the same app under a different domain) in my launcher and then reboot, all my PWAs and shortcuts are gone.
It does not seem to trigger with the other apps and shortcuts I use (things like linkedin, deliveroo or even this forum) but with the Etherfields app I have been able to reproduce it with every single attempt.
I can reproduce the issue both in main and secondary profiles (It does not wipe PWAs of other profiles though, if I create the faulty app in a profile all other PWAs in this profile will disappear but other profiles won't be affected).
For reference, I run the latest version of GrapheneOS (although it did also occur in the previous one) on a Pixel8 and my apps are up to date .
I only use Vanadium for my shortcuts and PWAs, I don't even have another browser installed. I do not create them from a private tab. And I use the original launcher. So this should be pretty much the standard/vanilla setup.