i have what may be somewhat of a temporary workaround. i'm unwilling to use wifi on my mx master mouse so i have this issue as well (shift key not working. one thing is i can hit caps lock for a capital letter which is likely the best workaround albeit unwieldy for more than a short string. i'm at an advantage because i type nearly 100% lowercase and thus i have the autocorrect 'capitalize' toggle turned off. but if you turn it on and type a word it will autocorrect to have a leading capital letter. this will only really be helpful for single words though and for sentences likely only capitalizes the first word.
oh, and i have a keychrom q1 keyboard connected via usb cable. so i have no idea why a bluetooth mouse would affect a key on the keyboard--i've seen a lot of strange stuff over the years and this is quite strange indeed.
i also had to reverse the scrolling to comport with my mac desktop. other than that, so far it's pretty nice--especially since i updated to the new ipad air and did a clean install and am having to set things up from scratch. /guy