I'd imagine they phased out so to say. Especially as enlistment papers seemed to expire every six months for one group or the other.
There are really 4 Continental Armies, that of 1775 (essentially the New England Militia), 1776, 1778 and 1780.
I posted the 1780 Orbat a while back:
Regimental Orbat of the Continental Army (excluding Regiments captured by the British or furloughed by the State of Pennsylvania):
Main Army (Washington)
1st Maryland Brigade (1st and 2nd Maryland)
2nd Maryland Brigade (3rd and 4th Maryland)
New Jersey Brigade (1st Rhode Island, 1st and 2nd New Jersey)
New York Brigade (1st and 2nd New York)
Light Division (3 brigades consisting of the Canadian Battalion and the converged Light Infantry of nearly the entire Continental Army)
Cavalry (1st and 2nd Partisan and 4th Legionary Corps)
plus 7 all French infantry regiments, all the French cavalry and artillery (a French Regiment was larger than a Continental Brigade)
Southern Army (Greene)
3rd Maryland Brigade (5th Maryland and 1st Delaware) - was not present with the army but was in Md guarding the LoCs of the main army (from which it was detached)
1st Pennsylvania Brigade (1st Pa and the remaining 2 coys of 2nd Pa) - again, in NJ
Cavalry (1st and 3rd Legionary Corps)
Highlands Army (i.e. facing NY) (McDougall)
1st Connecticut Brigade (1st, 3rd and 5th CT)
2nd Connecticut Brigade (2nd and 4th CT)
1st Massachusetts Brigade (1st, 4th and 7th Ma)
2nd Massachusetts Brigade (2nd, 5th and 8th Ma)
3rd Massachusetts Brigade (3rd, 6th and 9th Ma)
New Hampshire Brigade (10th Ma, 1st and 2nd NH)
Cavalry (2nd Legionary Corps)