I play Bellow's Breath repeatedly, once on battlefield A and once on battlefield B. My opponent controls both battlefields. On battlefield A, there are three units and a hidden card, which is Fight or Flight. My opponent reacts with Fight or Flight and uses it on one of his units, moving it to his base. Do I then have the option to choose which set of units takes the damage (either battlefield A where two units remain or his base where one of the units was moved)?

To answer your question: Yes, you do have the option to choose which set of units takes the damage for the first instance of Bellows Breath after the unit has been moved.

Here is the breakdown of how this interaction resolves based on the rules of Riftbound:

1. Targeting and Finalization

When you play Bellows Breath with Repeat, you make all choices (targets and locations) for both instances of the spell at the time you play it (Rule 746.2). These choices are locked in when the spell is finalized on the chain (Rule 352.14.b).

2. The Reaction

Your opponent reacts with Fight or Flight to move one of the units you targeted at Battlefield A to their base. Fight or Flight is a valid reaction that resolves before your spell. The unit is now at the base, while the other two units remain at Battlefield A.

3. Resolution of Bellows Breath

When Bellows Breath resolves, it checks the validity of its targets for the first instance (Battlefield A):

• Rule 356.3.e.8: If some targets become invalid, the instruction still executes on the remaining valid targets.
• Rule 356.3.e.5: Because the original group of targets no longer collectively fulfills the "same location" restriction, you as the controller choose a valid subset of the original targets to resolve the effect upon.
• Targeting Flexibility: Bellows Breath has no restriction preventing it from targeting units at the base. You may choose to have the first instance of the spell resolve against the units remaining at Battlefield A, or you may choose to have it resolve against the unit that moved to the base.

4. Summary

You cannot "follow" the unit to the base if you choose to resolve the spell at Battlefield A, but you do have the choice to resolve the first instance of the spell at either the base or Battlefield A. The second instance of the spell resolves independently at Battlefield B as originally chosen.

Note: I could not fully verify this ruling against the retrieved rules.