HelloPlease check, below link.https://bst.cloudapps.cisco.com/bugsearch/bug/CSCwo60906 Regards 

Can you try with this example,rommon-2> dirflash:vlan.datmanagedir800-universalk9-bundle.SPA.159-3.M11.binrommon-2> boot ir800-universalk9-bundle.SPA.159-3.M11.bin

Hello Kavish,Please upgrade from 16.9.4 to 17.3.X with disruptive mode.Once you have 17.3.X you can directly go 17.17.x with disruptive mode.if you want to go with ISSU, please follow below link for ISSU Support between ReleasesI have tested 17.12.5....

Yes, modules are hot-swappable in 9300https://www.cisco.com/c/en/us/td/docs/switches/lan/catalyst9300/hardware/install/b_c9300_hig/Product-overview.html.

Because clock is not synchronized and there is no reference clock.Could you check  IP's of NTP servers/peers and reference clocks are reachable from your device?