Assuming you were running the latest (1.14.N) jailbreak, you just need to
copy some backups ( rp/ && mkk/ ) to the userstore and reboot a few times.
The problem with a Factory Reset is that it wipes the partition which stores the jailbreak, MKK, and "gandalf" addon.
Yes, recent versions are resilient with an upstart script which can restore the jailbreak -- but that requires manual intervention, cf. the very great importance of MKK and gandalf.
A combination of Factory Reset followed by firmware update is an unilateral destruction of the jailbreak, with NO hope of recovery (unless your firmware can be jailbroken from scratch).
Avoid this at all costs.
tl;dr
Factory reset is BAD. If at all possible (unless of course something is seriously wrong with the Kindle, but you'd know if that were the case
), you should look for other solutions like
manually deleting your documents and Search Index folders.