Hi calmeg,
I'm not sure what's happening with your files. Which OS are you using?
I'm using XP. If I copy a file from my LW saved folder (not from the library, but from the saved folder) to My Music then I have 2 copies of that file. If I delete the file from my LW library (which also deletes it from my saved folder) then I only have one version of the file on my computer... the one in My Music.
*I do not have My Music set as my folder for saving/sharing within LW's tools > options*
Go into LW's tools > options > saving... do you have your My Music folder set as your LW save folder? If you do, this would explain why deleting files from LW's library also deletes files from My Music... whatever you delete from LW's library is deleted from the folder that you've set as LW's folder for saving
If you do have My Music set as your save folder, then whatever you save will go to My Music & will also appear in LW's library - that's just the way it works... LW's library doesn't hold the actual files but just shows you whatever's in your saved & shared folders. LW's library isn't an extra folder or anything - it just reflects what you have in your saved/shared folders.