I tested this again. I didn't realise that slipknot meant files that are visible only with the "~d=a" search. (I was actually able to make duplicate files to the main library by importing from the handheld folder.)
Here is what I did now:
1. Make a new empty library
2. Make a smartlist with this rule: [Media Type]=[Audio], named as "Audio Smartlist"
3. Make a smartlist with this rule: ~d=a, named as "DB All"
4. Make a new handheld that uses a folder (D:\HHD...) and syncs with the "Audio Smartlist"
5. Import two ape files from "E:\test\ma\" to the library
6. Go to the handheld and press "Sync Now"
7. Press "Recheck Sync"
8. Go to the "DB All" smartlist
9. Go to the handheld and press "Recheck Sync"
10. Go to the "DB All" smartlist
11. Go to the handheld and press "Recheck Sync"
12. Go to the "DB All" smartlist
13. Go to the handheld and press "Recheck Sync"
After four rechecks the DB All smartlist looks like this:
EDIT
It seems that these duplicates are only temporary. A restart of MC clears them.