As @alemabrahao advised, staged upgrades is the way to go. This lets you split switches in a network to be upgraded in grouped stages.   One thing to note is that switch stacks are treated as a single switch and therefore cannot be staged separately. All switches in the stack may/will reboot at the same time. ... View more

I agree with @Mloraditch, it does look like the firewall might be blocking something.  Are you in a position to monitor the outbound communications from the C9300s to see if anything is being blocked or timing out? ... View more