The fronts dont have center caps because of the locking hubs, the back has center caps that look like the locking hub, if that makes sense

 

 

I use Advance Autos plastic trim removal tools. That have a beefy one in the set that works great for this.

 

That tool looks a lot like a paint can opener...

 

 

To OP - yes there is a way - it's called caring and attention to detail. Between your wheels and the other member saying their center caps were not switched is so sad and totally unnecessary. I don;t understand how dealers can operate like this and expect it to be OK.
I would call them out on it as I know you planned to but I just wanted to add make sure they don't try to you its unavoidable. Aside from the above different widgets and ideas, even just a thick cloth will provide protection. Those are chips from the edge of a big screwdriver or pry tool which I have watched techs do with my own eyes. I pull hub caps off all the time for customers and have yet to run into that issue.
No excuse -

 

They are sending their wheel repair service guy to my house to repair them..... see how that goes..

Said there was no tool to take them off without scratches. Shut up when I pulled my tool for them out and a rag and showed can be taken off without damage.....

 

Dam, what a butcher hack job. Yes a rag works wonders lol.

 

I pull my caps off using a screw driver with black tape over the end before I let somebody rotate my tires. If I have aftermarket rims I remove the screw on caps before as well. "production" employees will strip the threads out on those, like they did mine