Are you using any mods?

Also: is it the save from previous patches? And were any mods used at any time with this save?

No current mods, this game save was started from version 2.0.8 (so I've played it through version 2.1.0h, 2.1.0k, 2.1.1 and finally 2.1.2b).

Around Level 9, while using version 2.08 I installed the turn-based mod.

...and not much later I then installed these 2 mods:
-UI Extensions
-CloserToTabletop

Once 2.1.0h was released, I discovered that the last two mods broke my save game, so I rolled back to an earlier save before I put those two mods (UI Extensions & CloserToTabletop) on, but there is a good chance that this current save did actually use the turn-based mod briefly.

However, I do have saves before installing the turn-based mod (I save every level-up), and to prove to myself it wasn't related to the turn-based mod, I loaded a level 5->6 level up and found that it also had the problem with the disappearing capital when going into the Settlement building screen.

I did actually forget that I'm using an older version of ReShade (Graphics mod, mostly use for the Clarity effect, and SMAA for most games) which I don't think is causing the problem, but I removed it before loading that older level 6 save to check and found the problem was still there.

I verified the installation just while writing this and that did not work, finally I rolled back to 2.1.1 and that works (Surprised that I could load a save created in a newer version of Pathfinder).

So version 2.1.1 does not have the disappearing Capital but version 2.1.2b does. This still could be related to a problem that started with an earlier version, I don't know if anyone else other than myself is having a problem in 2.1.2b with the capital building disappearing when going into building management for a settlement.

Have you tried asking the same question with this amount of details on Owlcat forums and / or in their discord? I think you have enough information for them to investigate and may be give some piece of advice.

I'm experiencing the same issue and there are people who also have it. It'll probably be fixed in the next patch. For the meantime you can force the capital to reappear by exiting to main menu and loading the game once again. If this doesn't help, exit the game and launch it one more time. Of course the capital will disappear again once you reenter it from the kingdom management map, but it's the only workaround as of now.

Thanks,

I also had a quick look at the Owlcat forums and saw a post from someone with a similar issue, so it's nice to know I'm not the only one having this issue.

Exiting to the main menu will be quicker than exiting the game, so I'll try that next time.

I just updated to version 2.1.3B today.

It doesn't look like the patch logs mention it directly, but the disappearing capital problem seems to be resolved in this version.

I'm impressed once again that this problem was solved so quickly, cheers Owlcat!