The UploadedQueries folder in C:\ProgramData\Bentley\OpmsServer\ contains files with ecquerries that are executed against the server during “reference out” operation. In order to remove old records go to OpenPlant Model Server Administrator toll >>> Locked Component Viewer >>>Checkout History. Any record in this list can be selected and deleted through right click context menu. When we create snapshot dgns or reference out, components get referenced out to dgn. This operation information is maintained on the dgn & corresponding entry is added in the database & file stored. When you hit REFRESH MY FILE, this information is pulled from the dgn & executed on server. So, when cleaning up, make sure, the entries are old enough than your referenced out /snapshot dgns.