Federation Commander

Just making sure I have this right.

Downed shields cannot have damage transferred off of them.
If you regenerate 1 shield box (during energy allocation right?), the whole bank is up though still damaged, and than you can transfer damage to an adjacent shield (assuming they're still up when you get to repair phase).

Not quite.

You are not moving shield damage around. Instead, you are moving undamaged shield boxes. So, if a shield is completely damaged, but either of the adjacent shields are not, up to five undamaged shield boxes from one of the adjacent shields can be transferred to the damaged shield. This covered in rule (3C3b) Transfer. Please keep in mind the other restrictions in that rule.

But again, you are transferring undamaged shield boxes, not the damage itself. (Though I guess the effect is pretty much the same.)