Thanks Doktor - I guess you'rereferring to the piston/valve phasing which is also effected by the position of the rod journal?
Sky bolt - The piston connects to the rod which connects to the crank rod journal.
All the piston/rod assemblies should be the same length.
If a rod journal is "out", then the total length is effected.
If the length from the centre of one rod journal is further "away" from the crank centerline, this means that this piston will not be in the same position for a given spot in the crank rotation, as all the others.
(Like a 4 spke wheel with one spoke too long or short)
This means two things:
1 - The piston attached to the effected journal aon't necessarily reach the same height in the bore, because the placement of the rod journal effects the total distance between the centre of the big end, and the centre of the piston pin.
Also,
2 - if the positon of the rod journal is not exactly at 90 deg to the next one, it also effects the timing of the sweep of the pistons. The piston attached to the effected crank journal will "throw" or move up slower or faster than the rest - like an out of balance Hula Hoop.
So the piston won't be in the right place when the cam opens the valve.
Probably the best way to think indexing is that it "degrees" the crank, rods and pistons so they all travel the same speed and arrive at the same place.
But because the problem is caused by the journals poisiton on the crank - it has to be done with machining and not changing the position of a timing chain cog.