The hosts had incurred a 10-point deduction for entering administration the previous day and further off-the-field problems meant it was only confirmed that City would be playing at the Ricoh Arena on Thursday.
Cyrus Christie bagged the winner for the Sky Blues after 13 minutes, and Flynn said: "The better side led at half time but we transformed it in the second half.
"We deserved to get something because we had that many golden chances. Unfortunately we didn't take any of them. We transformed things at half time. We needed to make changes and tactically I thought we got it spot on.
"They used the spare man very effectively against us and that caused us problems. They were better than us but we sorted it out and there were a lot positives in the second half.
"They (Coventry) most certainly looked like a wounded animal in the first half. They looked as if they wanted to put things right on the pitch and that is credit to the manager and the players."