A runner is on second base. Pitcher throws a pitch to the batter. Manager replaces runner at second with a pinch runner before the next pitch.Is this legal.?

No. A courtesy runner must be put in before the first pitch to a batter

Mannjo - You might want to look up the rule for whatever organizations rules you are playing under. SSUSA, NCSSA, and SPA all have slightly different rules for when you can put in a CR.

Mannjo.. below is the part of the rule you were asking about ..

8.5(5) • COURTESY RUNNER OFFICIALLY IN THE GAME
A courtesy runner must report to, and be acknowledged by, the umpire before play resumes. A courtesy runner may enter the game only prior to the first pitch to any batter.

a PINCH runner can go in any time ball is dead.

Curty you are correct. I overlooked the word “pinch”. Good catch. In this case it would be a sub which a team may put in at any time. Example being: I’m on second base and it’s 1-1 count on the batter. Coach announces Curty going in as a sub for stick. Legal. Curty would be in the game and stick is out of the game. But stick could re-enter at any time in which case curty could not go back in the rest of the game. (although curty could be a courtesy runner).
BJ, is this accurate? If not please summarize. Thanks!

Let me add that the person going in as a sub must be a player that is not in the game

yes curty is correct a pinch runner is a substitute player and may enter the game at any time