Fivespeed, I am pretty sure that you have a different issue than I do.
My 2014 Zero, after being very stable for all of its life, suddenly started showing charging issues very quickly once I started following Zero's advice and unplugged the charger cord as soon as the bike stopped charging - which could be entirely coincidental. Before that it spent 3.5 years plugged in 24/7 and charging would always finish at 100% on the display and 13.38 kWh on the app. But once I started pulling the plug, charging would stop at an indicated 92% and then it would turn itself on automatically and start charging again to show another 2% before turning off for the day. If I went back to keeping the charger plugged in all of the time, it would keep this up every day, until the charge would reach 98%, at which point it (and I) would finally give up.
It is my semi-educated guess that (in my case) one or more of my cells are charging quicker than the rest, resulting in a spike in voltage as the pack becomes fully charged, causing the charger to shut down. After a day, the goofy cell(s) have bled off some voltage, and the charger starts up again, charges another 250 watts, before shutting down and repeating the process the following day. I might also add that my bike has never had its firmware updated since it left the factory in December 2013. My solution to this issue was to give my 2014 Zero S to my daughter, who just rides locally, and buy a new 2018 Zero S.
I might also add that, other than a noticeable improvement in suspension and braking, the performance of my 2018 is very similar to my 2014 Zero. Even the range seems similar (even though it claims to have an additional 2 kWh in the battery pack), which I chalk up to Zero being more conservative in the range estimates shown on the display. On my 2014 S, the fun would end just as the battery display reached 0%, but from what I hear now, there is likely another 5 or 10% left in the battery pack as a reserve, once the display reaches 0.
In your case, it is possible that the firmware has either slipped a gear or you have developed some flaky battery cells. As for your software update taking all day and your shop requiring two weeks to get your bike back to you, that just doesn't sound right. What it sounds like to me is that the service department doesn't like working on Zero's and is making it tough on their Zero customers in an effort to discourage them in the hopes that they will go elsewhere.
I just had the 600-mile servicing performed on my new Zero, which it took less than two hours and was accomplished while I waited. This included checking for new software, motor commissioning and Zero updates on their website, as well as performing an additional 35 other physical chassis checks - or so the checklist I was given said.