you should have no changes made to the x/y/z steps per millimeter values - those are/should be constant. If you are using GT2 belts for x/y and 16-tooth with 1/16 microstepping your steps/mm are 100 ( read up RepRap Calculator - Original Prusa 3D Printers ). If you are printing a circle pattern and not getting consistent dimensions ( even if you over/under-shoot ) you have a few other things going on - most likely not a level bed or too much variance in your filament.
if you want 140 [mm] square and print 139.5 [mm] square, while the reprap settings are 100 [steps/mm] your new setting should be 100.36 [steps/mm], resulting in 50 more steps and the extra 0.5mm.
The belts and leadscrew accuracy should be close enough ( unless you have really crappy hardware ) to be within tolerances. The real issues as others have mentioned in the thread:
1) steps per mm for each axis based on hardware. Use the prusa calculator thats why he provides it!
2) tightness of the belts ( and anything else - there should be little to no play/wiggle ) and leadscrew / nut
3) esteps
I switched my X/Z chassis on my printer recently. The accuracy is just as tight was with the previous setup. All I had to change in the firmware/config was to account for tooth count of the new x config. The only pain point I had was getting the z min endstop positioned properly with the new setup - I kinda hate mechanical endstops for fine adjustment but the end result is worth it
Other factors which can contribute to this are many. I have found the most common one with something like this - bearings and linear rail are not in parity. EG the diameter of the linear rods is crap or you have crap bearings. Look for score marks on the linear rails - if you see them you have a problem! ( Other problems: stepper current, over-heating of the driver and/or stepper, crap steppers - I’m sure there are others )