The answer given is as follows: "Yes. The special rules in s 40-370 of ITAA 1997, instead of the general rules in s 40-285, apply to work out the balancing adjustment for a car you held where a deduction is available to you under Division 40 for the car's decline in value for an income year but you chose either the 'cents per kilometre' or '12% of original value' method under Division 28 for deducting your car expenses for the car for one or more other income years."
As a result of the issue of TD 2006/D17, TR 2000/6W (Income tax: substantiation rules: calculation of balancing adjustment for cars) has been withdrawn with effect from 3 May 2006.
For a copy of TD 2006/D17, go here
For a copy of TR 2000/6W, go here