I thought the update was supposed to process new resources without wanting to restart. I'm still getting the notice that resources will be added when the app is restarted. It seems to index somewhat beforehand so it's baffling. And since it is no longer a click to restart it becomes an extra step to close and manually restart.
My guess is that something still allows compatibility with older versions hangs up with Logos 6.3.
FWIW seems to happen on Win and Mac for me.