In the 2014/15 The FA Handbook (pdf).
In the section title Disciplinary Procedures - Regulations, pages 339-340:
Where a Player is charged with Misconduct contrary to Rule E1 of The Association, for a
matter on the Field of Play (which falls within Law 12 but was not seen by Match Officials
during the period of the game), the proceedings shall follow the specific procedures and
time limits set out in the relevant directions concerning such matters as determined by Council from time to time (the “Standard Directions – Incidents on the Field of Play which
fall within Law 12, which were not seen by Match Officials, but caught on video (serious foul play, violent conduct, spitting at an opponent or any other person, offensive, insulting or abusive language or gestures)” – see Schedule A).
Moving to Schedule A, page 347:
A Charge shall ordinarily be issued within the period of two working days of the incident
(i.e. for a Saturday/Sunday game, a Charge shall ordinarily be issued prior to 6pm on
the Tuesday). The Charge will be accompanied by all evidence, documents and written
submissions upon which The Association intends to rely.
Where the Charge is not accompanied by an offer of the standard punishment, the Charge
will state that The Association claims that the standard punishment would be clearly
insufficient, and will set out the basis for that claim.
In accepting the Charge, the Player may also accept the standard punishment offered, or
claim that the standard punishment would be clearly excessive having regard to the factors
set out at (d)(i) below.
In the event that the offered punishment is accepted, the suspension will commence
forthwith upon receipt by The Association of the consent of the chairman of the Judicial
Panel (or his nominee).
In summary, if the incident was missed by the referee, a charge would be sent to the club, and they would usually accept the charge, with the suspension added onto the end of the other suspension.
If it was a serious incident (ie. "the standard punishment would be clearly insufficient"), or the player appealed on various grounds (eg. mistaken identity, excessive punishment), it would be dealt with by the Regulatory Commission at their next meeting.