I've got a similar question. I'm on the .30 bootloader, which I've unlocked. I don't exactly remember why I'm on it, but if memory serves, before unlocking/rooting, I did the official upgrade to JB (which updated bootloader to 10.xx.xx) then I had to use the blob to downgrade to .30 in order to get the Asus unlocker to work. I've since flashed CWM Touch 220.127.116.11 and am running a fairly recent CM10.1.
So, am I now able to upgrade the bootloader to a newer (read official JB, or, more quantitaiively, 10.xx.xx) version? If I understand correctly, I can use a blob to flash a new "firmware", which would include the bootloader, rom, ril (we have these right?), etc. However, once I do this, I will be stuck on a stock recovery and rom, correct? If there is a way to upgrade the bootloader and keep it unlocked (/unlock it after), what are the steps involved?
I'm fine with the .30 bootloader, but it's ridiculous that the "Reboot to ..." options do not work. OK, so it's not ridiculous, it's just a bit inconvenient and has been causing me to not flash as many nightlies. My followup question would be, does the JB bootloader address this "issue"? And, correct me if I'm wrong, but the only way to get ROM Manager or GooManager to be able to do scripted flashes is to have these reboot options working, right?
TLDR: Have unlocked .30 bootloader, want JB bootloader but want it to be unlocked. Can it be done? Do I really want it?