Still having this problem.
Spoke with Japhy of tech support who recommended disabling plugins, and the problem didn’t cropped up for hours.
So I took it up with the Visual Arq folks who tells me there’s a reported issue with Rhino disappearing selected blocks, which is unrelated to Va. That thread is here, Objects Disappear when selected but the jetbrains link doesn’t work for me.
Since then I’ve reactivated VisualArq and while working most of the day the issue hasn’t occured again.