here is my experience...
360 #1 - banned/hdd disabled/gamertag corrupt, game saves show 'unknown profile', all purchased arcade games turned to trial
360 #2 - unbanned ixtreme 1.61, not connected to live for over 2 months, passed a repair request from xbox.com. Also keeping the top case off for easy flash access
I flashed #2 back to original benq firmware. Took hdd from #1 and connected to #2. Logged into xboxlive successfully (phew!) I did gamertag recovery and put email/password but kept getting error saying 'xbox live signup currently unvailable'
So i deleted corrupt profile but kept items.. then cleared the cache (hdd options x,x, rb, lb, x, x if i remember correctly)
After that I re-entered info and got my gamertag back. All game saves now show my gamertag instead of unknown. All arcade purchases turned to full game from trial. I also confirmed any games you save AFTER you been banned will result in a corrupt gamesave. Other than that, game saves loaded fine.
So in theory I think you could rack up achievments from an unbanned flashed box then load to a retail box... but you might have to do gamertag recovery each time... not sure about gamertag/memory card as i dont have one. Also I really doubt gamesaves could record any type of data that would indicate FW or disc id info. Only risk would be timestamps on pre-release achievments....