I'm having this exact same issue on my S5, though I am printing polycarbonate. Lots and lots of polycarbonate.
I never use tools to remove parts from the build plate, I just wait until the part cools and it detaches itself. The shear force of cooling must be hard on the borosilicate.
The part below was a 13-hour job consuming most of the build plate, so the bed was at high temperature for a long time. I use school glue for adhesion (since this is polycarb) and in general the part's pretty well stuck onto the plate until the bed cools.
I need to stock up on build plates I suppose!
(by the way, weren't we supposed to get aluminum plates a long time ago?)
You can see the divot below and also the piece of glass embedded in the printed part, which is kind of cool when you think of it.