You should get a replacement bike for the duration. I've had both my Gen 3 and 4 have warranty work. The gen 3 I had needed recovering and Roadside assist asked if i would require a bike and said they would deliver one to me! The Gen 4 (Present) also need a fair bit of work and Oxford gave me an R Nine T for a week, they said i could change if i wanted. But I liked the idea of trying out my inner hipster.
Hope that sorts the issue. I assume they checked the regulator/rectifier and charging circuit? My Biketrac unit does drain the battery if bike not used for a few weeks, but it shouldn't drain while bike in use.