There's no difference in meaning. There's a difference in tone.
"On the other hand" is good, normal, straightforward, standard English.
"The flip side" is informal.
Literally, it refers to the days of vinyl records, particularly the little 45 rpm disks that had one song on each side. You would play the first side, then you would flip the record over and play the second side. So the second side was "the flip side." Usually the song on the flip side was less popular.
"'We Will Rock You' was the flip side of Queen's hit song, 'We are the Champions.' To peoples' surprise, the flip side became an even bigger hit."
Figuratively, it can mean "the other side in a debate or argument."