I'm pretty sure that threat protection, content filtering, AMP and all those items only apply to WAN ports. I believe Site to Site VPN is considered a LAN link and then only those firewall rules that you setup on the Security Appliance>Site to Site VPN apply. Only thing I could find in the documentation is this "In a full tunnel topology, all security and content filtering must be performed on the full tunnel client. The Exit hub will not apply Content Filtering, IPS blocking, or Malware Scanning to traffic coming in over the VPN. However, IDS scanning will be performed for this traffic."
Adam R MS | CISSP, CISM, VCP, MCITP, CCNP, ITILv3, CMNO
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