I was playing with a friend on EU PVE Yesterday when we decided to sail back to a home port before a friend came on the next day & we came off Atlas at about 9 PM GMT yesterday.
I logged back in today to find our ship was destroyed and all our territory was stolen... Our ship was at full health and we left our base less than 24 Hours ago.
From my understanding it is 3 Days before your territory can be claimed.
So now a few days of hard work getting resources together to build a Schooner and all for nothing.
From Patch Notes:
V6.5
"PVE Territory can only be claimed if the owner has not been active around the territory within the last 3 days."