If you have an electrical fault it should only run only one bus flat -- leisure or starter.
The T 6.1 (which I presume you have -- you might edit your profile to improve the quality of assistance) will only charge the batteries to 80% unless you manually intervene by selecting max charge on the camping control panel and driving for two hours or more or plugging in th ehu.
If you have parked up for a substantial time with partially charged batteries the batteries will sulphate. Heavily sulphated batteries cannot be recovered. A layer of insoluble non-conductive lead sulphate covers the plates.
Suggestion: post detailed charge and park up history. Have you used EHU? Do you have solar? does your solar charge both busses? Were you parked up regularly? Did you use max charge beforehand? Have you had any inadvertent deep discharges? etc etc. This will help us gauge your battery state of health and potentially provide advice to prevent reoccurence.
It's also possible that one bus has recoverable battery(ies) and that VW has given you poor advice. What voltage and state of charge (bar graph) did your control panel indicate?
Another mode of failure of your starter battery that would fit these symptoms is a shorted cell on your starter battery. If so this would be almost certainly be a manufacturing or handling fault, both definitely claimable under warranty.
Summary:
- If all three batteries are faulty the cause is likely sulphation and very likely improper end user handling.
- If the starter battery is faulty but performs 'normally' at 10.7V it has a shorted cell most likely due to a manufacturing or (volkswagen) handling fault.
- If the starter battery is sulphated (won't take a charge) likely a parasitic load has flattened it. It might be recoverable with a good charger. Warranty claim is iffy -- relies on some electrical fault on the van being the underlying cause.
Another complication is that a shorted cell on a battery immediately results in an overcharge on the 5 remaining cells. So diagnosis is complicated and relies on knowledge that's pretty archaic.