shove an scp call at the end of your script and push them to the device?
You don't mention the operating system... Assuming linux:
scp /path/to/output/comicName.mobi /mnt/us/documents/comicName.mobi
then cause an index update via ssh
ssh root@kindleIP "dbus-send --system /default com.lab126.powerd.resuming int32:1"
Ref:
https://www.mobileread.com/forums/showthread.php?t=99746
It would pop to the top as "updated" assuming you sort by recency.
JB required.
(You might want to add Kindle Keyboard to your devices list)