I was using an old version (downloaded on 11/2015) of Pro Sites. Recently I updated the plugins on the site and noticed that most plugins (at subsite level, not at network level) were instantaneously deactivating and that I could no longer control the modules in Jetpack.
Time to re-subscribe to WPMUDEV and update Pro Sites. After updating Pro Sites, it worked - the probs above disappeared. But a new prob appeared: the dashboard and website of one (yes, only one) sub-site became inaccessible (500 error).
I cloned the site (using Cloner, of course) and that cloned site did not have the same prob as the original site. Then I realised I hadn't even picked a plan for it yet (so the site should not have gone live at all, right?). I picked a plan and --- problem's back (500 error for dashboard and site).
So then I deactivated Pro Sites - and problem's gone again. That solves the prob for now.
But I do need to use Pro Sites. So what do I do?