Yes but it won`t affect balance. Reciprocating weight IE: crank, big end of the rods and the flywheel and front pulley on the V612 motors are the things that are critical. All pistons in as set are balanced. In any event true balance is only at a particular small range of RPM.
Swapped the crankshaft from a S engine (bought new without flywheel or pulley). I’ve been asking local machine shops if I should balance this, and they said that only if pistons are weighed differently.
Rotating mass - front pulley, crankshaft and flywheel usually are balanced as an assembly if you are building a highly spec engine. However, easier said than done. I have mixed cranks, pulleys and flywheels for a daily driver without serious vibrations.
If you have a 3.0 liter flywheel and front pulley they are the same regardless of S or whatever.
If you have a thick flanged 2.5 liter I can lighten it and balance it with a fixture designed to return the 2.5 after lightening to the correct "offset" balance.
A early thin flange 2.5 will not be usable with a 3.0 liter.
Now do you have correct coarse or fine thread flywheel bolts to match the new crankshaft. Early ones had M10 coarse thread later ones have M10 fine thread and different lengths for 5-speed or automatic transmissions.