I see that this post is old, but I thought I would pontificate a bit. Maybe someone else has a similar question.
The system I'm using is an OLD xorcom system with a sbc re-branded as xorcom and a xorcom usb channel bank. The whole thing was originally sold as a system. When I got it from a friend of mine, it had the original software on an internal cf. I swapped out the cf for a larger one and upgraded the RAM. I've had a LOT of trouble keeping this thing stable, so that's why I'm chiming in here.
Over my short, exasperating involvemnent with asterisk/elastix/freepbx I've had to start over quite a few times (mostly because of dahdi issues). With the cf especially, re-installing and reconfiguring can be a time consuming task (and not all that fun). In order to save myself a lot of time, I decided to start imaging the drive to have a fresh, quick-to-deploy backup. I've been creating image files on a large drive and then I can just load it back onto the working drive when things blow up.
Imaging the cf wasn't as easy as a regular hdd (making reloaded images bootable was complicated as I recall) so a while back I switched over to an external usb ssd drive. The difference is pretty remarkable in terms of how fast things load and reload, but I must say that the cf worked fine.
My system has an on-board cf slot and it sees the cf as just another drive. If you're using a usb connected flash drive adapter I'm sure you'ld be okay assuming your motherboard supports it.