Made an account just to throw in my own experience here. Been experiencing the same behavior since about April or May 2026.
Device is Pixel 10 Pro, just updated from GrapheneOS build 2026070501 to build 2026071101 and experienced the behavior yet again.
Using Niagara Launcher, issue occurs with both Vanadium and Brave PWAs.
On startup, shortcut and icon are briefly visible, then disappear. Tapping the shortcut at this time pulls up a Niagara error: Error - Shortcut isn't available.
Differing from Russpelz most recent message, my PWAs did not disappear after a non-system-updating restart.
Using Private Space and work profile via Shelter, but Brave and the PWAs are all in the Owner profile.