That sucks they scored your bike up. What I do if I ever have to leave a bike is make a video of it with my phone, right there outside the service bay, a sort of visual scan. And I explain to that them I don't mean to be rude but I've had bad experiences in the past, and this is my way of making sure there is evidence that my bike was damaged in the shop. It puts them on notice. I do the same thing when I bring in a wheel to have a new tire mounted. Its not just the video, its them SEEING you make the video.
Personally it doesn't bother me that the charge level rises a bit after the bike is used... I just assumed all the batteries have to level up somewhat.
As for the disks I had the same miserable experience and had to replace both of them. Here's the thread in case you are interested. Check the markings on the disk in particular and see if you have this version of them.
https://www.electricmotorcycleforum.com/boards/index.php?topic=10895.0EDIT: Nm you posted in that thread so you have already seen it. I'll leave this here in case anyone is curious.