Are you playing on hard or something? It's really hard to die, especially in Route B, when playing as 9S otherwise due to how OP hacking is. I kinda get it though, the last thing you do in Route A tends to drain a lot of your restore items, leaving you lacking until you get to a store. I learned my lesson since then to not be cheap and just buy a lot of them so I never come across such an issue again. But yea, if the lack of restore items is that frustrating, just put it on Easy for the meantime.
Some of your sidequests will disappear once you reach the part of the story that has you in the (Very minor spoilers)
City. At that point, they will not be available to you until Route B, which will allow you to do them again until you reach that point again, as well as give you sidequests that are exclusive to Route B. But there are sidequests exclusive to Route A, basically stuff only 2B would realistically be doing, like a quest for Operator 6O for example. Route C also has its own exclusive sidequests.
That said, no sidequest is permanently missable.