From the 'Board Level Annotation' docs:
Board Level Annotation gives you complete control over the annotation in your project with annotation settings saved in an *.Annotation text file displayed under the Settings\Annotation Documents sub-folder in the Projects panel. Altium Designer manages Annotation files automatically.
It sounds like somehow the .annotation file was removed from the project. Or maybe the project file was renamed, but the corresponding annotation file wasn't. If you can find that file, possibly in an old copy of the project, you may be able to add it back in to the project. But if you've made other changes to the design since that file was lost, things may get trickier.
But after playing with this, it looks like there's a relatively easy way to solve this, as long as the PCB still has the correct designators. If you do a PCB -> SCH design update, it looks like it will rebuild the annotation file automatically. This won't update component classes to reflect the new designators, so you'll need to do a SCH -> PCB update afterwards to handle that, but once you do everything should be back in sync with the old designators. If you've added any components you will need to do a board level annotate on those (you should be able to pick them out specifically in the Board Level Annotate window to do that). Depending on what kinds of changes you've made and how out of sync the designators are, it might be simpler to go back to the previous project version, make sure the annotations are correct, and then re implement whatever changes you need.
What I am not going to do is randomly re-annotate and then the PCB layout is all wrong.
Just to be clear, re-annotating should never compromise the layout -- it will of course change the
designators, but it won't, like, swap component positions all over the board because the designators changed. Components are linked by their unique IDs, so as long as those are correct the layout and connectivity are safe. Worst case, if you can't recover the old annotation file or a version of the .PcbDoc with the correct designators, you could go through the board component by component and manually edit all of the designators, then do another PCB -> SCH, SCH -> PCB update cycle.