Has been done before, e.g. Robert Leroy Anderson:
As investigators searched Andersons truck they discovered several receipts for duct tape, black water-based Tempura paint, paintbrushes and a bucket, most of which was purchased a few days prior to and on the day Piper went missing. Investigators suspected that the paint was used to disguise Andersons Bronco. Their suspicions would prove to be correct.
They called in experts to analyze the paint job on the truck more closely. Samples were taken and chemically tested. They found that the Bronco had been painted with the same material bought by Anderson around July 29th. The paint used was a kind that could be easily applied and washed off.
Interestingly, a witness claimed that he saw Anderson cleaning his car on the same day Piper disappeared. It was believed he was washing off the paint and ridding the car of any other incriminating evidence.
(Source:
http://www.trutv.com/library/crime/serial_killers/predators/robert_anderson/index.html - quoted part is on page 3)
I thought of this right at the start, when it seemed the perpetrator (if there is one) might be a painter, but I think he would've covered the visible spot of primer as well. However, the van might have a new permanent color by now.