This is a thoughtful response but, once again, attributes the differences to the incorrect causes. Break in is generally ascribed to the formation of the dialectric charges in wires, circuit boards, caps and resistors. It generally takes a short time for the dialectric to form, perhaps from a few hours to a couple of months, depending on design and materials used. If a component is not used for a time the dielectric charges can break down and some further short period of break in will be required. If you ever buy a really old piece of gear that has been sitting and plug it right in, the piece will hum as the caps have lost their dielectic charge. To reform them you must apply slow, progressive increases in voltage. This is a completely different thing than the break down of solder joints and circuit board traces which, as pointed out, may take years. Let me explain one aspect of this. In any wire, some of the signal is carried at the surface of the wire. This is a known phenomena called the skin effect. The same would hold true of a solder joint, some of the signal travels on the surface. As environmental factors, and even the certain chemical components that may be present in the solder begin to oxidize the outside of the joint the signal is now trying to flow through metal oxide and environmental pollutants such as cigarette smoke and gasses released by the heating of the wire insulators within the component. The resistance to the signal can become significant and even rectify the signal in some circumstances. Do an experiment. If you have and old pair of interconnects that you can screw with reflow the solder on both ends of just one cable and compare. The results will be similar to what you describe in your tonearm fix. I might add that the very small voltages resulting from the output of a cartridge are particularly suseptable to these types of problems. Don't forget that the output of the cartridge may be amplified from 40 to 70db or so. The greatest overall amplification anywhere in the replay chain. You can bet if there is degredation you will hear it. As far as the replacement of the insulator is concerned, the air in the honeycomb that you removed is considered the least sonically intrusive dielectric material. The silicone that you replaced it with is considered to be far inferior sonically. Again, when you do your interconnect experiment after being done with the first comparison, just slather silicone onto the fresh solder joints and listen again. Components, like listeners definitely degrade over time. I know that I have. It's just reality.
Marty