For the past couple of months i had been experiencing the same problem. IMA battery almost always in regen and from time to time (on the same trip) total loss of charge.
Measuring the small 12V battery showed a decrease in charge (a little over 12V). I tried force regen a couple of times and it made things better for a couple of hours and then again the same situation.
Took it to the dealer today, put it under HDS and it showed decreased charge in a couple of systems as well as the 12V battery (11,7 Volts after a 5 km drive). Dealer put the battery in a charger for a couple of hours and then i drove off. Things were pretty much OK for an hour or so and then again the same sh*t.
So i went to a local battery shop to purchase a new (bigger battery). Since Cobb and other folks here recommended going to a 51 class battery we tried with that option. But with no success. No matter how we tried we could not squeeze a 51 battery in there. Even after removing the original battery base and case we faced up with two problems: 1) the 51 battery (being bigger in every sense) was pressing firmly against the air intake/filtre. Something i did not like a bit. 2) The 51's ends were thicker and more "up" making it impossible for the existing electrode ends to attach to the new battery. Of course we could have taken it to a nearby car electrician and find a solution by changing electrodes and battery case but... i was tired and bored already. So we fitted a new Bosch battery (same as stock in specs), payed 60€ or 81 bucks and i went my way.
I drove for 25km and the result was amazingly different. No drop in IMA charge below medium level and it was supporting more the gas engine.
Now, i know that a few cycles are required to achieve optimum equilibrium between the two batteries but i think a solution has been finally reached.
that i had the same problem last year and back then dealer changed the 12V battery with a new OEM one under warranty. This latter battery lasted one year (20K km approx) exactly before it died. Let's see how far i can go this time...