Is Keeping Factory Paint Important?

Yes and PDR can save factory paint

Golf R GTI glue pullling paintless dent repair saves original factory paint

Strength and Adhesion

Factory paint has the best strength and adhesion, because factory painted topcoat is cured at a higher temperature. In factory the curing temp is in the range of 350F. Conversely, aftermarket paint is cured at most in the range of 150F. The higher the temperature means more chemical cross-linking can happen in the topcoat. The more cross-linking reaction means more strength of the clearcoat and better adhesion. Chip resistance is far better with factory paint than aftermarket. 

The example above: Even after being sideswiped there was no damage to the factory VW paint. 

Even after strong glue pull procedures the paint remained intact after the paintless dent repair.

Audi Q7 large dent paintless repair removal at customer home to save factory OEM paint repaint and door replacement

Colour Match

As a former automotive painter, I know how hard it is to match colours. Even if a spectrometer can match and mix the colour to 90% accurate, it is often necessary to blend the adjacent panels to ensure the 10% is not visible. When the adjacent panel is blended, the whole blended panel is clear coated. This means repairing a dent conventionally usually requires two panels have all trim removed, blended, and fully re-clearcoated. That's a lot of dependent operations to be executed perfectly to get a perfect repair. The probability of a perfect repair is very difficult in a complex process.

The example above: the SUV would have needed a new door skin or shell with a 3 panel outer paint job (also inner door) to remedy in a conventional auto body process. That's a one week repair. With above PDR example it was done in one day with no complications of replacement and repaint of the conventional process. That's value just in the down time saved and obviously saving potential paint issues for 3 outer panels plus inner.

SUV roof caved in repaired with paintless dent repair to avoid cutting, welding, and repaint. PDR saves trade in value

Loss of Value for your Trade-in

When you trade in a vehicle that has a insurance claim and a repaint, you typically lose 10 to 15% of the trade in value. On a $20,000 trade-in that's $2000-$3000! If the conventional repair was done through insurance then it's easy to research via insurance records. However even private repairs can be detected. It is in the best interest of trade-in appraisers to use paint measurement tools to check if any extra paint (or filler) has been added with a film thickness gauge. If extra thickness is detected from any previous repaint repair, they have an excuse devalue your trade-in. Do you want to have maximum trade in value?

The example above: the caved in roof of the SUV would have conventionally needed to be cutout, new skin welded back in, then repainted. There could be filler and primer needed to correct any issues during the weld install. Typically a $3000-$5000 repair. That would have been extremely invasive  to original conditions and would have heavily depreciated the vehicle. Who do you trust more the OEM assembly plant to install the roof skin correctly or the local bodyshop? Whenever welding is involved be aware that rust is a real risk near all the welded areas.