Close the file on the server. Name it as xxxx old.fmp12
Open the file and do a save as compressed xxx.fmp12
Open xxx.fmp12 on your server.
Best is to move the xxx old.fmp12 off the server and onto a device with Pro installed. Save your copy and then move the copy back onto the server.
Even if you do not plan to use any of the tools, deleting records won't affect the shown file size until the file has been closed on the server.
You can simply do this from the admin console, close file open it again and you should see the file size changing.