The Fortress skeletons are NPC characters created by the game to protect Fortresses. 

The Temple
The Temple has 15,000 skeletons initially
The skeletons will not re-spawned after being killed.

War Zone Fortresses

The War Zone Fortresses have 15,000 skeletons initially
The skeletons will not re-spawned after being killed.

Homeland Fortresses

The Homeland Fortresses have 15,000 skeletons initially
The skeletons will only be re-spawned in the fortresses owned by the defending faction to fight against invaders.
The skeletons will re-spawn after being killed, but at a slow rate once every hour.
When the defender takes back a homeland fortress, the skeletons will not be re-spawned immediately after the fortress is conquered. It will be re-spawned at a slow rate once every hour until the skeleton count reaches the cap again.
Note: this applies to all fortresses within the original 5x5 homeland area of the defending faction, regardless whether they are inside or outside of the faction border. 

For example, if the defending faction took back a fortress in their original homeland area, the skeletons will not be re-spawned right away and the invading faction will not have to fight skeletons if they can conquer it soon after. However, the longer the defending faction holds their own fortresses, the more skeletons will be re-spawned in the fortress to protect it. 

The Citadel
The Citadel has 30,000 skeletons initially
The skeletons  will only be re-spawned in the Citadel owned by the defending faction to fight against invaders.
The skeletons will re-spawn after being killed, but at a slow rate once every hour.
When the defender takes back their Citadel (before the region is lost), the skeletons will not be re-spawned immediately after the fortress is conquered. It will be re-spawned at a slow rate once every hour until the skeleton count reaches the cap again.
If the Citadel region is lost to the invader, the faction is defeated.