Just make sure any production server doesn't use the same connection as repository before you start to delete tables
. Btw if you have a simple way to reproduce your situation you could create a step-by-step guide or create a video - it should help get to the bottom of what has happened.
The resources project is meant to keep all other things a DB repo would normally keep that are not solutions (styles, information about DB connections/column info and settings, users/groups, ...).
When you create a new solution you can use the same resources project, especially if you are going to deploy the new solution to the same application server as the previous active solution (so both will use the same repository DB when deployed).
If you want your solution to use other styles, DB column information (including Servoy sequences, default values, dbidents, ...) you can create and use a new resources project.
Yes, the Solution Explorer node for Resources does not change label. Only the tooltip shows the name of the workspace project that is being shown and used by the currently active solution. I'm usually not that interested in the name of the resources project after I initially link a solution to it. Activating another solution will automatically activate and show the contents of it's referenced resources project.