From the Doc:
Counterbalancer Update for 2001 and early 2002 models
The single bearing counterbalancer was replaced with a double bearing counterbalancer in late 2002. Counterbalancer failures were experienced on some 650's and on a lesser amount of smaller displacement engines. A counterbalancer assembly is available to upgrade to the double bearing version. Included are: Counterbalancer, bearings, circlip and shim. The 2003 counterbalancer cannot be used, as teeth on the counterbalancer sprocket have a different mesh.
470/501/550/650-2001 use update part # 201 257-01
470/501/550/650-2002 use update part # 210 243-01
Complete counterbalancer removal
Since the counterbalancer can be a potential source of engine failure, serious racers sometimes remove the counterbalancer completely to eliminate the hazard. This does result in more vibration at idle and at very low RPM. In place of the counterbalancer a 7.4mm spacer ring should be used. The balancer drive shaft gear teeth can be ground off. Set crankshaft axial freeplay to 0.6mm-0.8mm. Use main bearings SFK NJ2206ECP/C3. The crankshaft can be rebalanced if desired.
Noises from the starter area
The free wheel mechanism (clutch) that was introduced mid 02 is built into the starter reduction gear set which was previously a solid machined gear assembly. It's recommended to fit this to earlier machines to prevent gear/sprague breakage if kick back occurs. As far as the Sprague assembly itself, the large outer gear/hub is the same 01-03, the sprague is the same 01-03, but the inner small gear/hub is different mid 02. Why? The gear teeth pitch was changed mid 02 on the counterbalancer, inner counter balancer drive shaft gear , outer balancer drive shaft gear, primary gear, and outer clutch basket gear. Mix 01 and 03 gears and it's very noisy. The noise usually happens when an 03 counter balancer is installed in an 01. It would have been nice if one could simply change the balancer drive shaft with it's machined-on inner gear to an 03 assembly, but the 01 outer balancer shaft drive gear will not fit the 03 drive shaft. Install the outer 03 balancer drive shaft gear and you also need to change the primary gear. clutch basket, and the inner starter sprague gear. Paranoid types will start thinking 'conspiracy theories' at this point. (Actually they make a special double bearing balancer with the 01 gear pitch.) All this info is because if your 01 hasn't been updated, it can't be the freewheel mechanism that is slipping because you don't have one. Probably the sprague is slipping. They are quite delicate and small amounts of wear on the inner gears hub or the outer gears hub will make the sprague itself slip. Remember that the outer hub is the same 01-03 but the inner is different (DSducati).