You need to do what you say you can’t do in your last line, but you need also use the Media Manager to create a new offline sequence where you’ve deleted all the unused media from it.
Select your sequence, then choose File->Media Manager…
Choose “Create Offline”
Select your sequence preset
Turn ON all the remaining checkboxes, enter your desired handle size.
Save the new project file.
— Wes Plate
Automatic Duck