I think I figured it out. Seems that where you stick the dedup is important. So posting this works:
index="Firewall" AND host= AND "PHASE 2 COMPLETED" | dedup s2s_VendorPeers | stats count(s2s_VendorPeers) by s2s_VendorPeers, _time | convert ctime(_time) as time | fields time, s2s_VendorPeers
Where this doesn't:
index="Firewall" AND host= AND "PHASE 2 COMPLETED" | stats count(s2s_VendorPeers) by s2s_VendorPeers, _time | convert ctime(_time) as time | fields time, s2s_VendorPeers | dedup s2s_VendorPeers
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