I had a creature on the board the enters with two -1,-1 counters. I had removed one of the counters so it only had one -1,-1 counter on it. I then flickered it with "Personify" and it returned to the board with one -1,-1 counter. Flicker effects should remove all counters, then the etb should trigger and have it re-enter with two -1,-1 counters. there is no reason it should ever re-enter with the same number of counters it left with.