My understanding from reading here is that if you rearrange your samples (change name, move to another folder) then the m:s keeps track ok. It works because each file is internally identified by a unique signature (a ‘hash’) that is derived from the audio content.
Interested to find out what happens if you try to delete a sample that’s being used though.
EDIT: See also
EDIT 2: The definitive story from the manual.