I dont think its an issue, but i really don't know. You should file it truthfully anyway. As far as I know, there are not specific instruction on when filling AC21 should be done. There is even different openions on whether AC21 filing is mandontory, some attornies say not filling is ground for denial, many people here seem to have used "tell if asked only" policy. Your decision should be whether you want to file AC21 or not, but I dont see you have any choice about filling AR-11 using company B.
With AC21 specific details, an attorny would be the best person to give you peace of mind (although i think that if you ask 5 different attornies you will at least get 2 different openions.
Please keep in mind that this an amature taking a crack at the situation, I would not take this as an advise, just as an openion to consider.