I thought that was a nice touch and I imagine it was paying respect towards those who lost their loved ones and the firefighters who sacrificed so much on 9/11/01.
I imagine the American flag COPS logo was used in the episodes filmed right after the 9/11/01 attacks.
I don't remember it being used for the John Walsh Jacksonville episode, it's been years since I last saw that episode of COPS, I used to watch America's Most Wanted back in the 90's, I wish they kept the American flag logo longer than they did, of the main logos I liked the one used from Seasons 2-9 the best.
It was used near the end of that episode. I'm betting it might have been accidentally placed in a syndicated edit.
I prefer the blue logo better than the bland white logo. At least with the white logo, they added the cool police light effects. I did notice the logo starts out blue during the Spike/Paramount Network run.
I thought the logo for the Cops Reloaded spinoff was very cool and liked the effects used there, as well as the sounds.
I did enjoy the cool police light effects on the episodes starting at Season 10, I thought it was interesting see the logo change on the Spike/Paramount seasons, I also noticed the COPS logo became a darker blue color sometime during Season 8.