I was testing in creative and managed to get my befriended mob killed by an Alex Mob's crocodile.
When it died I noticed that the respawn token you get wasn't labeled with anything.
After respawning her, it consumed the item and once she took damage the game crashed with this error message.
[18:25:40] [Server thread/ERROR] [ne.so.be.BefriendMobs/]: Befriended mob "Wither Skeleton Girl" missing owner. If this happens not on initialization phase, maybe IBefriendedMob#init() wasn't called on init.

I would definitely test to see if it was a creative issue, as I tested it on survival and everything seemed fine, including when they got murdered by a crocodile again.

EDIT: I tested it again in creative from dying to a normal death and they do indeed link, however when I tested the crocodile death again the data was wiped again.

This is what the item looks like