Before the 3.0 update came out I had all my dlcs and the Isle of Siptah on an external hard drive on my Xbox Series X.
After the 3.0 update it said I did not own the isle of siptah when I did. But still would let me play on it.
So I reinstalled all the DLCs into my internal hard drive and the Isle of Siptah and it fixed the invisible animals and creatures.
They are all now visible the way they were. Doing this also fixed many other problems that came up after the 3.0 update.