Your understanding is correct. If the H9 is in Pre/Post mode and your preset is set and saved at Pre, H9 i/o 2 should pass the signal unchanged. A few questions to get started:
1. Is your amp's loop serial or parallel?
2. Does this occur with any other algorithms on H9, or is it exclusive to Phaser?
3. Is the feedback a quick burst, or is it just constant once you engage your loop?