Some of it may depend on the copyright protection on the files. I haven't tested that.
All my files are from my own CDs so I have never had a problem connecting to a computer that doesn't contain files on my ipod. I can still sync other files without it deleting files from my ipod that are no longer in my itunes.
Links to deleted files still exist in itunes until you delete them from itunes. It might cause error messages if you try to play them when itunes can't access them. I discovered this when deleting duplicate files. I had itunes find duplicates, deleted the actual file using file manager then went to itunes and deleted the link that gave me an error that file was not found.
You may find you can transfer to a new disk. Reset your library and then not have an issue when you turn the drive off. Itunes isn't checking all the links so it won't care unless you try to access that file.
The simple way to test this is move the location of a file you have in itunes and on ipod. See if this causes issues. If not, then try multiple files.