Hooray! You should do a cold restart to make sure everything still works with an empty Flash.
A bit more on how this all works: Your Poseidon configuration is saved in a combined config file/executable. Can't recall the name off the top of my head, but running that file will bring the stack online, and I believe the Poseidon installer adds it to user-startup by default. So that might be why your USB stick shows up on a no-Flash boot. As Darrin says, you can run without the Flash completely if you prefer.
Because your settings are in that one file, if you change the configuration you need to re-upload the Flash to make sure the USB drivers are receiving the right settings from a cold start.
So it sounds like you've got a good, safe config file. Now you should be able to run Quick Setup from the Luciferin menu to have everything important automatically set to get uploaded to Flash.
One question, though, have you had your USB stick plugged in this whole time? With Poseidon's default settings, my machine would hang with a USB stick inserted on boot. Something to do with timeout settings. Changed those, re-uploaded the Flash, and now everything works. I wonder if you were running into something similar?