External Drives and Cleaning Library

Hi,

All my video files are held on external drives; I have one for movie rips and two for tv shows.

The movie drive has two folders; 'archived' (my collection) and 'new' (for us to watch).

I've successfully scanned my library to jukebox for the movie drive, however, after watching a new movie, I then move it to my archive. This is simple enough when then updating/cleaning the library, however, for my scraped tv shows (across two drives), if a select 'clean library' it then deletes all my media on the external drives.

How is best to go about managing my set up and not loosing everything that's scraped from external drives which requires updating/cleaning?

Thank you