Eagles of the other battalions were to be returned but this decree was impossible to implement immediately, and as late as mid-1809 there is evidence that regiments still had all their battalion's eagles, and drapeaux, with them on campaign.
As far as battalion fanions are concerned, Article 18 of the decree says that each service battalion was to have an enseigne of unspecified design. The appearance of these enseignes was never, is seems, described properly, although by May 1808 proposals had been made about cost. In April 1809 Napoleon wrote that they were to be "very simple" and without decoration, "bearing only the number of the regiment and the battalion.". Examples that are left are uniquely different to each regiment, presumably designed at the whim of the colonel.
The Modèle 1804 eagles continued in use until replaced by the Modèle 1811 eagles. Article 7 of the Decree of 25 December 1811 specified one eagle per regiment - the new eagle was a lighter version as the Modèle 1804 was considered too heavy. Article 9 stated that the eagle was to be carried by the 1st battalion of each infantry regiment and that other battalions were to have fanions without inscription.
The Decree of 1811 also specified the colours of battalion fanions at Article 10; 2nd battalion white, 3rd battalion red, 4th blue, 5th green and 6th yellow. This scheme had already been described in a letter from Berthier to the Duc de Feltre on 23 October 1811. The decree went on to say that no importance was to be attached to the fanions. In other words they were not eagle substitutes. The staff was finished with a simple iron spear point.
The Modèle 1804 drapeau (lozenge design) continued in use until replaced by the Modèle 1812 drapeau (tricolore design). The design of this drapeau was discussed through late 1811 and a decision arrived at by 8 February 1812.
Modern authorities include Hollander, Regnault and Charrié.
JC