I think this conversation overlaps - a lot - with re- and retro-bolting. Often times, my issues are the same.
Here are my considerations for removing bolts:
1. Are they dangerous? Old, rusted, etc.? Then they get the chop and usually replaced.
2. Will removing them scar the rock further? This is LNT applied to the vertical. I know of one crag that I won't chop a squeeze-job because I don't think I can keep from damaging the rock further.
3. Were they placed by the FA team, or are they sanctioned by the FA team? If the FA team is unreachable, I ask the local community for an opinion.
4. Is there adequate traditional protection nearby that can substitute? Sometimes the FA team had good reason for not using that crack, so I like to try to ask them in consideration #3.
This is just what I consider when removing or adding bolts...
Oh, and about the tuning fork. Let me ask around. It was my understanding that it would work, but you're right about 5-piece bolts. I'll ask a few people wiser and with more experience and let you know what I hear...