Hey man, i just did the factory reset through the phone, not the boot menu, maybe someone could chyme in and say if there is any difference?
But very shortly after I logged back into my phone with google, all my apps were downloaded and installed back on the system, and everything you've downloaded that for whatever reason may not reinstall is in your "my apps/downloads" or whatever it is in the market, it's all tied into your account
KEEP READING:
Just a heads up, and I asked earlier whether there was a difference between the boot menu wipe and the HTC built in factory reset, because I did the reset last night, and with in an hour had a reboot, and have had it reboot yet again today at least once that I've seen. It's not as bad as it was yesterday where it was rebooting 3x in a row or something absurd, I swear I had a dozen in the day..
All that being said - from what I've been seeing it's an issue with the Verizon Towers not our phones, hence some areas are unaffected and they just haven't rolled out the tower updates to the areas yet, and once they do the rebooting goes away. It is a pain in the nuts, no joke... and I can't say it was worth it because I've still had reboots.