So I finally got my 2017 FXS 6.5 Modular back this past week. Only after getting Zero to push the dealer along did it finally get looked at, BMS issue found, part ordered and finally installed. 7 weeks total. The dealer took about 4 weeks before they finally looked at it. The BMS was ordered and after a week I emailed Zero to ask if the BMS was shipped. They immediately replied and shipped the BMS to the dealer by UPS Red. Dealer then took 2 weeks to install the part. I've learned that if that dealer tells you they are 3 to 4 weeks out but to bring the bike in right away because they might fit it in, get a solid appointment and bring it in on the day of the appointment. Or perhaps use a different dealer.
This weekend I had the chance to take it out for a longer ride. I did a little riding during the week so I'm not sure how many miles I put on it. But it took about 8 hours to recharge and the two batteries took 5.15 kWh per my Kill-A-Watt meter. I guess that is about a 10% loss from nominal 5.7 capacity.
I also noticed while charging one battery was a bit warmer than the other. My infrared thermometer showed 105 deg F on one battery and 100 deg F on another. The Dell XPS 13 computer that I use also charges at about 100 deg F too. So I guess I'm not too surprised, just curious why one battery is warmer than the other.
The last thing I've noticed is that the BMS logs started with the date 12/31/1969. I am guessing that there is something the dealer didn't do when installing/initializing the BMS. Not sure if it is important or not though.
I am happy that both batteries are now working thanks to the help of the people at Zero and the Zero warranty that covered the BMS.