The 25-year-old joined the club on loan from Peterborough United last month, but has managed just 92 minutes of football since completing his move on January 4.
"We've had numerous chats with Emile. It's difficult for him to have come in at the time he did because the team have been winning," Flynn told the The Star.
"That's made it very difficult for him to break into the side. My advice for Emile is when the opportunity comes for him to take it.
"He will certainly have a big role to play between now and the end of the season. I say to players that every game is 14 v 14 because you have the opportunity to play three substitutes."
Doncaster currently sit second in League One.