Flinders, voted player of the year by both the players and fans last season, holds the club record for the total number of clean sheets - 49 - and is one game away from overtaking Norman Oakley to become Pools' record holder for the number of league appearances by a goalkeeper.
"We're very lucky to have Scott," Cooper told the club's official website.
"Knowing what was coming I didn't say anything about his 200th game during the week because I wanted him to remain focussed, but after the game I made a big show of it in the dressing room.
"Two hundred games for Hartlepool and 49 clean sheets in the league is an outstanding contribution.
"One thing I knew when I came in to the football club was that we had an outstanding goalkeeper at this level in Scott - and that's no disrespect to Andy Rafferty, who has been a fantastic number two in the last few years.
"I think everyone said to me during the summer that we had to hang on to Scott - well, we are and he's proving his worth and he will continue to do so.
"He's a very under-stated character, he doesn't shout from the rooftops, but he works ever so hard and is very proud of his achievements, and rightly so."