Thomas, 24, replaces Kayla Rendell who has been ruled out by an ankle injury.
Charles and Rendell follow Lotte Wubben-Moy in withdrawing from England duty, after the Arsenal centre-back pulled out because of a foot injury.
The England squad arrived at St George’s Park on Monday as they face successive fixtures against the French.
England host France at St James’ Park on Friday 31 May, before travelling to Saint Etienne on 4 June.
The Lionesses have four points from their opening two games in Group Three, following a 1-1 draw with Sweden and a 2-0 win against the Republic of Ireland.
The top two sides in the four-team group qualify automatically for Euro 2025 in Switzerland, with the other teams going into the play-offs.