Haven’t ran in to this issue myself, but does resetting wg connection (from within gh-action) not work before executing deploy?
➜ flyctl wireguard reset <org-name>
New WireGuard peer for organization '<org-name>': 'interactive-agent-<user-identity>-RANDOMBASE32'
I don’t think one could do much other than complain, but I expect Fly to sort this out, given that this issue is inherent in their software and architecture.