Fortresses respawn at random intervals, ranging from 3 to 24 hours after looting.
Look for the green spotlight from them.
When this happens the landscape around the fort and its structure will also revert back to original.
Do not put a portal too close or it will be gone.
Duplicate spawns
Be aware that the ballistas can respawn several times so you are fighting a stack of them at once - getting hit by 5 or so javelins at once can be a rude experience
Apart from the above respawn rates - the fortress inhabitants and ballistas will respawn in 30 minutes and be ready to kill you.