Guys, I think you may be barking up the wrong tree here. Firstly, a bad LED doesn't start working again, so unless there's a bad solder joint, its come 'n go behavior must be coming from elsewhere. Secondly, because of the additional AUX output jack that is operated through the footswitch, the on-off footswitch LED does
not use the typical mechanical bypass switching set-up found in most BYOC pedals. Instead, it uses a version of the "Millenium Bypass" electronic switching scheme, which is significantly more complicated. It is less likely, therefore, that the fault is in the footswitch, and very possible that a solder joint or one of the components in the Millenium Bypass circuit is the issue. Check out the schematic and labeled PCB diagram
HERE. The Millenium Bypass circuit is shown at the lower right corner of the schematic, just above the title block. It involves lug 7 of the footswitch, the LED (D9), a 1N4148 diode (D8), a 1K resistor (R64), a 2N5088 transistor (Q8) and a BS170 MOSFET (Q9). So quite a few solder joints to check, as a starting point....