The old Dino Storage mod is still running in the background even though all souls have been converted.
Despite the change to Dino Storage V2 many players are still using the outdated soul storage and could lose dinos once the old mod is removed.
To avoid such issues you need to destroy your outdated soul storage after you took out all of your dino souls.
After that just go to engrams and learn Soul Traps (DS), Soul Terminal (DS) and Soul Gun (DS). Then build a new Soul Terminal (DS) and store your (converted= dino souls in there. Every soul that should still be managed by the old mod will display an "OUTDATED MOD" note behind the dino's name (which shouldn't be the case fr anyone as we forced V2 to convert all souls). If your terminal is still from the old mod version it will also have an "OUTDATED MOD" note in its name.
So, to make sure you're not running into any problems, please learn the new engrams and update your terminals in the next 7 days.