My guess is NO. :)
I have a couple of opened up S9 (not S9+, which is why I’m only guessing) and the water seal is placed to the side of the hole where you would have inserted the tool. I put a tool in there and wiggled it around and could do nothing to the seal.
Also, the seal is very delicate so even if you break it, you would not feel it, so I have no idea what the “jerk” you felt might be.
So again, I guess you didn’t damage the water proofing but, just in case, don’t go swimming with the thing. ; D