Well in my case it isn't about the restart or plug back USB warning.
I have my profile in 512MB memory unit or the HDD and I use a separate 16GB flash for save modding and dlcs.
Besides the restart or plug back warning once in a while, I have never had any problems with the drive corrupting itself if I just pulled it out. I'm not dumb enough to pull it while ingame, saving or while it's accessing it. I pull it while in the dash or turned off.

May I repeat myself. Now with the new dash, everytime I pull the usb, use Horizon and plug it back into the xbox on or off, the flash stops working and shows as USB storage device, as if not configured. Plug it back a second time into the PC, Horizon hangs and doesn't detect it as a xbox flash. If you open it in explorer there are some corrupt directory and file names instead of the usual data001, etc. And I have tested it many times, pull while on or off, inject or mod save with Horizon, plug it back while xbox on or off and in any of those combinations the USB end up unrecognized by the xbox and you need to configure it again.

On the other hand using the old usbxtafgui so far I haven't encountered this problem, but need to test further.