These zones are completely out of action, you can't attack from or to them. Factions are also given one turn to join the zone back to their main land, or the zone is awarded to the faction with the most borders surrounding it*.
You can use this mechanic so you can focus war assets on less zones, and get a positive outcome.
A longer explanation
Ubisoft has an online view for the faction map, which has a history of the seasons.
All the following turns are based on season 1 turn 1, as it's yet to be completed as of writing this. Following are some occurrences of this happening:
Turns 1 - 3.
On Turn 1 the Knights and Vikings swapped a tile.
On Turn 2 both these zones were gray zebra striped out.
The Knights attacked, and took, the Viking zone next to it.
On Turn 3 both the zone they'd attacked, and the separated Viking zone were given to the Knights.
Turns 3 - 4.
On Turn 3 the Knights and Vikings swapped zones, the Vikings was not connected to the main land, but the Knights was.
This meant the Vikings was fully surrounded by Knights main land.
On Turn 4 the Vikings took an adjacent zone and connected it to their main land.
Turns 5 - 7.
On Turn 5 the Knights took a Viking zone, but the Samurai cut the zone off.
On Turn 6 the Samurai took a Viking zone, to control three of the four adjacent tiles.
On Turn 7 the Samurai's were awarded the zone.
And so we can guess at the basic functionality of this.
But there may be a couple of edge cases that we've not seen, and I've not guessed.
How do those territories come back into play? Will another team be able to gain control of that territory?
Either a faction rejoins it to their main land, or
they are awarded to the faction with the most zones around it*, after being out of play for one turn.
Is it strategically good or bad to have territories like this for your team?
I'd say it's good, if the faction knows what it's doing, take Turn 9, and ignoring Turn 10:
The Knights surrounded three of the Samurai's zones.
On this turn they could have taken all three of the Samurai's zones by focusing on just four zones, the two the Vikings took, the only non-taken zone and the one above it.
If the Samurai took more zones, then they'd be cut off and awarded to the knights, due to this mechanic, and it's easier to bulk up four zones rather than focus on nine.
The Samurai on the other hand only needed to focus on three zones to gain one zone in the long run.
Of the three zones that were surrounded by Knights if they'd had given up on the one closet the Knights base,
protected the other two of the three and taken the single zone below the closest to the Knights base.
Then they could have taken the two zones below their line, and lost the one that was cut off. Ending in +1 territory.
Only focusing on three of the nine zones.
Both these examples are ignoring Turn 10. But I think the faction would have to protect the core zones for another turn. And so the Samurai probably should have won. This didn't happen however, the Samurai took some of the Knights zones, and auto lost everything the round after.
* We don't know how this works if there are even territories around the zone.