[Heavy-matill]

You are right, annotations are generally not lost, but they are also not merged with in 2-Way-Sync:

Device:
 - Song 1 (last changed 2h ago)
    - File A (last changed 10d ago)
      - Annotation X (added 5min ago)
    - File B.v3 (last changed 1s ago)

Cloud:
 - Song 1 (last changed 1s ago)
    - File A.v2 (last changed 1s ago)
    - File B.v2 (last changed 20s ago)

If i sync in either direction, obviously the state is copied correctly. 
Device -> Cloud: I now have Song 1, File A with Annotation X and File B.v3 in the Cloud (as well as on the Device), so yes Annotation is kept
Cloud -> Device: I now have Song1, File A.v2 and File B.v2 on the Device (as well as in the Cloud), Annotation is lost

2-Way-Sync now only looks at change date of the Song and keeps the one in the Cloud, because it was changed more recently. However it keeps that Song together with all its files and their annotations. Result is the same as Cloud -> Device, Annotation is lost

What I want is a deep 2-Way-Sync, where the Date of the Song might actually be ignored. Instead File and Annotation lastModified time are checked. 

e.g. if File A and File A.v2 have the same Id, the one with the more recent change is kept, in this case its A.v2 (Cloud -> Device)
For File B its the other way arround, because the file on the Device is newer than the one in the Cloud (Device -> Cloud)
The Annotation does not exist in the Cloud, so it should be copied there as an Annotation for File A.v2.

Final outcome would look like this:

Device & Cloud:
 - Song 1
    - File A.v2 (last changed 1s ago)
      - Annotation X (added 5min ago)
    - File B.v3 (last changed 1s ago)