A boat that is currently in repair box 3 and is being repaired and moved to box 2, can I roll again to move it even further?
Good question, the Section 10 rules are silent on this.
The way I have been playing it (only been playing for a few weeks), is that each Submarine in a Repair (or Ready) Box only gets one roll per week. Otherwise, it is conceivably possible for a Submarine to go from Repair 3 to Ready for Sea; which, does not seem historically accurate / correlate with the chronology/events of the U-boat War.
My thinking: A Submarine in Repair 3 is just one step away from being a Total Constructive Loss (not economic to repair), so it is pretty bad shape. Even if the shipyard put every available worker on the project, it is hard to image a boat going from that sorry state to crewed, provisioned, armed, trail runs complete, and secured for sea in 7 days.
The Commentary in Section 9.0 (although not rules) seems to further support the multiple weeks are required approach.