I'm pretty sure it will stay after Richie comes back, just like the "just me and you" ad-libs in I'll Be There For You that Jon brought back in 2011 during Richie's first absence remained when they hit Europe.

To my knowledge, the acoustic intro was first (and only) done in Denmark in 2008, on that day Jon and Richie were inducted into songwriters' hall of fame, so made this special version of Prayer, dedicated to Desmond Child. It's a bit different, as it started from the bridge (like in acapella), not from the first verse, but the basic idea is the same. It only returned in Edmonton 5 years later for a second time! Correct if I'm wrong. Check the video, shitty audio, but that's the best I could find. There used to be a better quality version, but it was probably removed not too long ago, cause it used to be one of my favorite performances of this song. I'm really glad that now we have a chance to hear the acoustic intro in much better quality!