Hi Barry
This is my view only from what I have read, but when dealing with Napoleonic eagles and flags etc, that we must consider the eagle itself seperate from the flag. The eagle was only carried by the first battalion, but other battalions also carried Fannons or flags either 1804 or 1812 or 1815 design on ordinary flag poles.
The flags and fannons were probably carried all the time, and was up to the indivudal unit commander wheather they obayed the official edit or not (can compare this to Louis XIV wanting all French cavalry officiers to wear the cuirass, and it being largely ignored by them).
As for the Eagle itself, in my view this largely stayed behind, and certainly post 1812, but again was up to the whim of the unit commander. If you consider the disasters that happened to the French from 1812 onwards, capturing an Eagle should have been fairly common, but do not hear of many cases.
For light infantry battalions skirmishing, I agree with you. The standard practice was for half the unit to skirmish with the other half in reserve in close order, and this is where the colour party should be. But there are always exceptions!
As for painting the extra companies for the Flanquer Chasseurs, I would since most of the campaign's they fought in would have been from 1813 onwards. You could also look at the units average strength, most middle and young guard battalions were only 500 strong, wheather they had 4 or 6 companies.
Hope this helps!