The English flag (St George's Cross) was adopted in 1191 I can find no reference that says it ever contained a fleur de lys.
As England was invaded by the Normans in 1066 it might be fair to assume the Normans brought it with them, but they didn't as their flag/arms contained lions. The fleur de lys, whilst an ancient symbol, wasn't used by French royalty on their flags until the 12th century.
There is a use of the fleur de lys in England and that is on a Royal Coat of Arms, Edward III quartered the English Arms with the French to show his claim over France in 1340.
The fleur de lys was removed from the Coat of Arms in 1801 when George III abandoned his claim to the French throne.
The flags are modern, although they are based on the coats of arms of the counties. As pointed out, the use of the symbol was intended to show that France was an English possession. Apparently, it also represented the sixth son.
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