Usually an upgraded catalogue is given a name like the LR3 one, but with -2 on the end of the name. You'll also expect to find a previews folder also with -2 on the end.
For now, don't start Lightroom the usual way. Instead, double click each lrcat file, ie a catalogue. This should start LR4. If it asks you to upgrade, you know it's an LR3 catalogue. Exit, noting the folder/name. Afterwards, you can delete these LR3 catalogues or make them read only in Finder, but not yet.
If you're not asked to upgrade, it's an LR4 catalogue. Decide (common sense) which catalogue is the correct one - I'll call it A. Again, close and note the details. If you're lucky, there's only one catalogue that looks right. If not, and you have managed to add work to more than one, open catalogue A and use File > Import from Another Catalog to bring catalogue B's contents into it. After doing so, set catalogue B to read-only via Finder or delete it, so tidying up as you go.
If this catalogue A now shows every picture you expect, that's great. If not, maybe you have other LR3 or LR4 catalogues which need importing into the main catalogue? Follow the same method as above. Each time you open a catalogue, ensure you know which one it is (tip - customize the identity plate in each one).
At this stage-
- do not use Folder Synchronize to get yourself out of this mess
- do not use File > Import Photos to fix it either
At this stage they are more likely to compound the problem. Only resort to them if you are certain there are no other catalogues which can be imported into your main one.
For now, forget the metadata update indicator. It doesn't really matter.