Wales still lead Romania by a point at the top of Group 10 but the Romanians have a game in hand, which should garner them three more points against Bosnia-Herzegovina.
That means Wales are likely to travel to Romania two points adrift and knowing only a win will be enough for the play-offs.
"We have got another chance out in Romania which will be very difficult," Flynn added.
"Romania have only conceded one goal in the competition and are a difficult team to play against and they showed us that respect, and you have to take your chances at this level.
"The positive thing to take from the game is that we have shown Romania that we are capable of beating them.
"I would have worries if we were going to Romania with no chance, but we have."
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