Hi Ann,
I'm not sure I've ever had to do that before, but here's my supposition. The ATAP activation replaces the running database process (binary) with the Guardium "version", so if the other databases use that same binary then they'll need to be shut down. If they are using a different instance or binary then you would probably be safe to leave them up.
Like I said, just my supposition.
Matt
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Matt Simons
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