Everytime you download/Link from Ancestry or upload/link from FTM is a NEW Tree/FTM Link and creates a new tree in the target location. At this time there is no way to relink.
Open FTM and go to the Plan Workspace on the Current Tree tab. It will show you which Ancestry Member Tree it is linked to. You can delete the extra ones.
FTM controls the Link/Sync. Decide which FTM file is working for you, the rest are unnecessary to keep, unless they contain information you need to move to the working tree.