If I have 2 units on the battlefield, and the enemy uses Bellow's Breath, and I react with Flash to move those 2 units back to my base, do they still get damage dealt to them?

Yes, both units still take damage.

Bellows Breath targets the units themselves, not the location — and when both units move to your base via Flash, they are still at the same location (the base). Since the base is a valid location for Bellows Breath to affect units, all targeted units there take 1 damage each. The "same location" requirement is a targeting restriction checked when the spell is cast (both were on the same battlefield, so it's fine), not a resolution requirement. At resolution, the spell tracks the units to wherever they are, and since they're both at the same base, they both get hit.