Whenever upgrading app to newer version of Mendix, new local copy of app is created.
If app name is Test-main and on upgrade it creates a new folder as Test-main_2 and so on.
If the project is already migrated to latest version then these old version folders are of no use and this creates unnecessary folders and also becomes difficult to find right folder if there are too many of such for a particular app. It would be good if the same folder gets replaced by the new version while upgrading.
May I ask how you upgrade? Because I have never seen this to happen. When I open the newer Mendix modeler and open the project which is on an older version that project will just get updated and no new folder is created. It will only create a new folder if you open the teamserver project again that you already have on your local disk.
So I wonder how you end up in this state.