Same issue. Did a two week "dry run" of GrapheneOS, back in November/December, before making the switch. Ran into this issue, with both stock launcher and μLauncher, which was a disappointment.
"Oh well..."
Clean slate, GrapheneOS for real since 1½ months now. Did add a few PWAs, but was wary due to the previous experience.
PWAs stayed safe though! "Huh, I guess the bug has been fixed then!"
After all, there's been a few new updates to Vanadium since.
Until today. Poof! All gone. Only change that was made before reboot is that I added a whole bunch of new PWAs — trusting the bug was no more.
I can thus only assume that there seems to be a correlation with the amount of PWAs on launcher before the bug triggers.
Unfortunately, I'm unsure of the PWA count before or after the incident today. But I'd estimate I had 6-8 PWAs when everything was stable, and was probably up to 20-25 now...
I suppose it could be an upstream bug, but whatever the case it seems fitting for GrapheneOS to focus on as PWAs are likely more popular with the privacy/security crowd.
Hoping I may have shed some light on the issue, in case my hunch is right.