I always assumed that the batteries were powerful enough to allow both jump drives to be used consecutively (i.e. you can do a jump-3 and then a jump-2).
This does raise the question of why have two jump drives at all (and if you do, why have one Jump-2 and the other a Jump-3, although the deckplan indicates they are both identically sized).
My handwave answer back in 1980 or whenever I first ran it was that each jump drive has to be run off its own set of batteries which are recharged simultaneously (with presumably a third smaller set that powers the other ship functions) but that obviously isn't going to work with a Megatraveller or TNE design (these people are Tech level C - they must be able to build a single battery array that can switch power between drives).
Unless maybe there is a real issue with the reliability of the technology and they had to build two jump drives as a fail safe.
'Zero point energy accumulators' most of the google results I get for those look like crank science to me... and if the Traveller Universe had something that could regenerate power without any fuel source, why would anyone mess around with fusion plants and fuel that can take up 50% or more of a ship?
Of course exactly the same applies to solar-battery powered ships like the AN, sure they may have to sit in-system longer to recharge, but given that solar power is 'free' and there is no need to waste time docking at space stations or skimming gas giants to refuel, I can see they would almost certainly be more viable economically on longhaul routes (50% of a jump-5 ship is fuel tankage and once you take out the drives, powerplant and bridge that leave s very little space for passengers and cargo).
Running cables from the small craft? - unfortunately the AN needs 60 tons of fuel to make a Jump 1, and the pinnaces can only carry a fraction of that.
While trying to deconstruct the ship using Book 2 it did however occur to me that you could have added a powerplant-J (there is plenty of room where the hydroponics are), put 120 tons worth of collapsible fuel tankage into the cargo hold and you would then have the reserve capacity to make yet another jump-2 and to run a proper maneuver drive.
My current working solution to the Annic Nova mystery was that the ship was actually built by a Sargasso of Lost Starships colony that cobbled it together out of several vessels that had got there and then found they couldn't leave due to there being no source of L-Hyd fuel in system (whether you can have a humanoid population with no water is another question - however I suppose you could visualise a lone desert world with no accessible moons, comets or gas giants where water is fanatically hoarded (like Arrakis) and actually serves as currency - and then someone arrives expecting to buy however many hundreds of tons of the stuff that you need to fill a starship's tank...)