I think Bobby was primarily kept around because he and Jon used to be really good friends (and Phil had confirmed that Bobby was essential in terms of keeping the humour up in the band and his vocal contributions). He also used to introduce him onstage as "my good friend Bobby Bandiera..." in later years.
But I'm also quite certain he kept him after the HAND tour in order to have some sort of safety net in case they had to make it through one night when Richie couldn't play. Maybe he had at first even thought that Bobby could handle lead guitar for a couple of shows if needed, we don't know that. After Puerto Rico he certainly knew better. And anyone who had seen Richie deteriorating from early 2006 up to the unplugged show in 2007 can understand that it would've been quite naive to go on like "yeah this will work".