@Rui Moura If the two battalions were deployed separately, as happened at Bussaco, which battalion held the flags, or were they split between the two battalions?
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Only one Portuguese Battalion of the Peninsular War was awarded a Flag for distinguished services in the field of battle. But that is another story.
@paul.d.leeson Flags were only honour of the Regiments. Two flags each Regiment. A Royal flag and a Regimental flag.
The Portuguese Regiments of the Peninsular War were always organised in two Line Battalions.
Here is an example of the Royal Flag of the 14th of the Infantry of the Line in the book "O 14 de Infantaria" (Rui Moura, 2009)
Book for free download here: (https://www.academia.edu/43319488/Regimento_de_Infantaria_14)
A good paper on the subject from @Robert Burnham can be found here https://www.napoleon-series.org/military-info/organization/c_portflags.html
Note: JPR in the corners below the crown stand for "João Príncipe Regente"