Here is an account of what the ship went through after the war:

https://wwiiafterwwii.wordpress.com/2015/06/23/uss-prinz-eugen/

While it did spend extensive time in US Navy yards, I am not sure it was ever repainted. No specific mention is made in the article of that happening. There are black and white photos of it, and the paint scheme doesn't look altered.

That said, under "Destruction of USS Prinz Eugen" in the link above is printed:

"Professional to the end, the remaining Germans onboard repainted the SCR-584 haze grey so the Army OD green would not stick out."

That was an Army radar brought aboard, described in the text. The Germans decided to paint it. The article does not specify whether they used possible stocks of German paint which might have been aboard, or US Navy paint, and "haze gray" is enough of a "generic layman's term" for a warship paint job that there is ambiguity in how the author means that. Another possibility is that, while the overall ship might have been in German paint, the Germans used US paint, feeling it was better than the Army OD color. If you look at DKM and US late-war neutral gray colors, there are close smiliarities. A US gray color might have been "less offensive" to their sensibilities than OD.

Also--as noted in the article--markings were painted on the hull to judge listing after the blasts.

So, except for one highly ambiguous little detail, and some markings, I have found no other mention of a big repainting. It seems if they knew they were going to sink it, they would not have bothered to paint it all up? I have found nothing conclusive, and allow for the possibility it was, but personally feel they did not. That is only my opinion, for the little it is worth.