Provided the wiring is rated for the current, that length should not make much difference.
Is the problem affecting all axes/motors?
Did you fit a different power supply when you moved from 48 to 24V?
Given the time frame involved, it sounds like something failing/jamming once it gets warmed up. If it's only one axis, have you checked that axis for any mechanical problems?
If it's all, the change of sound from the steppers could be something like the power supply failing, but if you've swapped to a completely different supply, that should of ruled that out.
As a start, I'd be monitoring the power supply voltage to see if it changes when the fault occurs.
I'd also be trying to spin the steppers/screws by hand with everything cool/powered down, and then spinning them again after powering down once the fault happens to see if there's any noticeable difference.
It may also be worth removing the steppers, checking the couplers are ok (if you have slotted alu style couplers, they are bad for splitting and giving strange faults), and spinning each axis by hand to feel for any binding/roughness.
It's always worth spending a bit time covering the basics, before digging too deep for faults.
Moray