Very mysterious dropping steps on one Y axis motor...I'm starting to lose it!!

[JAZZCNC]

M-C has probably given you the correct answer to your issue in that it's a step timing issue because even though you swapped motors and drives you will have kept the same Step settings in Mach3 and the drives will both use the same pulse edge setup meaning the issue will remain on that side.

Without getting too technical what's happening is that the STEP pulse is given in front of the DIR pulse so any steps given before the direction change are lost.
The cure is easy just change the Active state of the STEP pin in Mach3 just for that side,

The test is like M_C describes with small moves back n forth (bounce test we call it, see vid), 10mm is more than enough but I would do more than 100 as it's easier to see then. Notice on the video the indicator doesn't get touched until it's finished and goes back to zero slowly for the last move so the indicator doesn't get knocked.

This test is worth doing on all your axis because it doesn't always show, esp on a Z-axis that doesn't change direction very often ie Profile cutting and pocketing where it just goes to depth and stays there until finished. Often problems like this only come to light when someone tries to do 3D or engraving work with lots of Z-moves.

Dazp1976 point is valid also because 48V is low for a Nema 34 motor so you could be dropping steps depending on how you have the machine setup, esp on a rack n pinion setup which is very inefficient compared to ball-screw machines and have a lot higher friction to deal with. At higher feeds and with a heavy gantry on an 8x4 machine, you could easily be losing steps.
Try running slowly and see if you are still losing steps, this will tell you straight away if you are dropping any due to lack of power/friction.