I dunno if JEmplode does this or not, but it should. Otherwise, the reboot may happen before the flash has been completely written.

Jemplode does not reboot the player after uploading an animation. I hand-rebooted the player myself using the Hijack menu option for that purpose. However, I will concede that I might have done so too quickly. I did wait a few seconds (maybe as long as 20-30 seconds) after the upload was complete before rebooting the player.