I was ticketed for allegedly going 59 in a 40 zone today. However, the officer showed me the radar and it read 52. I challenged him on this and he said that it was because he got me at 59 the first time but then had to re-calibrate and I had slowed down to 52 by the second reading.

He told me to choose option 3 and fight it in court. The way he said this almost seemed like he wanted me to read between the lines ("... choose option 3 and we'll fix it in court if you know what I mean"), as if he's implying that the ticket will be dropped if I fight it.

There is no code R, or reduction indicated.

I'm going to first request disclosure. If the notes do indicate 52 instead of 59, then is this grounds for the ticket to be thrown out?

Getting multiple readings is common. Some officers may include all readings, most just write the highest. There's nothing abnormal about what happened.

Ok. Is there any way I can discredit him on the 59 reading? Even the officer admitted verbally that he could not lock in my speed at 59, and had to recalibrate.

There's no requirement to lock the device at the highest speed obtained. It's quite common to clear a locked speed to see if someone is speeding up or slowing down. There's also no requirement to show you the speed displayed on the device.