I have two profiles, but I hardly ever use the secondary one. I mainly stick to my main profile where I have all my PWAs installed.
I can't really pinpoint a specific set of steps to reproduce the issue. I simply install PWAs from Vanadium and place them on my 'desktop'.
Whenever my phone battery dies or I restart it, some of these PWAs mysteriously vanish. It's a real hit or miss - sometimes only a few go missing, other times it's all of them, and occasionally none disappear at all.