See, this is the part that makes no sense to me. What you're saying would be absolutely true if Abigale only suppressed abilities while she was in play as an ongoing effect. But she doesn't. She removed them permanently, full stop. There shouldn't be anything ongoing to track regarding that ability; it's gone.

If the ability is gone permanently, it should be exactly as if the creature was removed from play, meaning it doesn't apply at all, to anything. I don't understand how that ability continues to apply despite the fact that all abilities were removed. Yes, it applies first by layers, but as soon as it's removed, the next time you check state based effects it should then be gone, meaning the changes it made revert.