For me a random stronghold fixed the issue with the new patch arrived today. Completed the stronghold and now its back on the map.
If you have any of the Strongholds missing from your map, do the following steps. This should add that specific Stronghold back for you.
Have a Friend invite you to a party that has a Mission for that Stronghold active.
Run through that Stronghold on any difficulty.
Once completed, go through the normal end mission screen.
Once back in Fort Tarsis, either start an Expedition or go to your Javelin and select the Stronghold on your map
The missing stronghold should now be back on your map.
I'm now having this exact same issue...got in a finished load of the temple and now two hours later its missing from the map. Help..
It shows that the mission (the stronghold) is completed in the challenges tab, maybe that's the problem, missions completed are not possible to be done again, despite it being a stronghold.
I tried quickplaying Strongholds and got Tyrant Mine, but it was bugged. Only 7 of the 12 shaper fragments appeared, so it couldn't be progressed. I was forced to abandon it. Tyrant Mine did not reappear on my map. Maybe it will if I get a non-bugged session and get to play thru it, but with random strongholds, that could be a long process to test that theory.