Time machine over samba, "The identity of the backup disk has changed"
Edit: Find my solution below.

I have the same problem on Raspian with a Ext4 file system (no LVM). Samba is version 4.8.5, compiled from source by myself. MacOS is High Sierra, backup is encrypted.

Time Machine pretends to have finished the backup successfully. When it starts the next time, the message about the changed identity appears. After choosing "backup anyway", it creates a completely new backup in a new sparse file. (Like @thaimin described it). 

On the Samba mailing list someone states: 


  Recompile samba with  --enable-spotlight and all works.


That is not true in my case, because I did compile Samba 4.8.5 with this option (what I didn't do is setting up tracker as suggested in this blog post).

Workaround

I compiled Samba in the previous version (4.8.4). Now it works as expected (same system, same dependencies, same configuration).
Someone already created a bug ticket for Samba.