[AtlUmpSteve]

Let's start with some basic rules.

A legal courtesy runner must be a player not currently nor has ever been in the game. The FLEX is in the game, so cannot be a courtesy runner.

You stated the DP is pitching; if that is for the FLEX, and the FLEX is not playing defensively elsewhere, the FLEX has left the game. But, that isn't mentioned, so I hope it isn't the case, since the FLEX can only reenter once!!

So, assuming the FLEX is still playing defense somewhere, then the FLEX running for the DP is a substitution for the DP (if DP is not on offense, the DP has left the game. When the DP returns to pitch, it must be reported, and the starting DP has used her one reentry.

When the FLEX runs a 2nd time, that is also legal, but it is, again, a substitution for the DP. That player has used her one legal reentry, and may not reenter again. The team may now enter a substitute, and that person is now the new DP, and/or may use any player currently in the lineup to pitch. But the starting DP is done for the game.

When you allowed the second reentry by the DP, that was incorrect. And this was an illegal player, that could (should) have been appealed by the opposition.