I thought I would share with everyone what I did this morning in hopes that it will help if it happens to anyone else.
I was/am on Apex 1.3.0 with the .320 leak applied, however I wanted to clean-up all my apps so I figured it would be nice to have a clean .340 back-up of the basic OTA. So I started by doing a factory reset.
I then updated the bootloader and rebooted, no problems.
I then updated the kernel and rebooted, no problems.
I then updated the baseline and rebooted, no problems.
I then did a data and cache wipe and updated the system .340 and rebooted.....oh crap! I am booting in to the bootloader screen. This has never happened before so I freaked out for a moment and then remembered what I had read before. I had a copy of RSD Lite 4.8 with me at work and TBH's .320 SBF. So I got everything ready to SBF my phone for the second time (the first time was just to go from the leaked 2.2 back to 2.1 to get the OTA). I had no problems and after about 10 minutes everything worked fine and I was back up and running.
The one thing I noticed was that the kernel was not updated anymore, but the bootloader and baseline both were updated. So instead of trying to use the system zip again and since RSD was already up I found the .340 system only SBF and used that with no problem.
Then I rerooted with z4root, no problems and downloaded clockwork recovery and then reapplied the kernel. Rebooted and now I am up with the .340 OTA rooted. I have made a back-up and have flashed Apex 1.3.0.
I was hoping that I never had to use a SBF to get my phone back working, but I did today and it worked just fine. Not that I wanted to go through this everyday, but it is nice to know with what I have learned from everyone on here and all the tools that the developers have given us that this can be done.