Can I use the same pre-authorised scanner to scan all the VPCs in my AWS subscription?
If you have VPC peering enabled between the VPCs, yes. You would deploy 1 scanner into a VPC with access into the other VPCs, then create connectors for each VPC and scan them using the 1 scanner.
This document explains step-by-step how to scan peered VPC's: Scanning Peered VPC's
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