I did something similar. I used floor wax remover on a set of Centennials and thought that nothing would remove the yellow color in the balls. Tried everything I could think of for about one year. Nothing seemed to work.
Then I used Aramith ball cleaner in my new mechanical ball polisher. I put a drop on each ball and spun for about two minutes and then wiped off the cleaner with a towel. Repeated about five to ten times and the yellow stains came out. The balls diameters did not reduce as measured by a caliper.
I don't think it matters what machine you use. I do think that Aramith cleaner and several applications will remove the yellow stains.
After about two repetions I noticed that the stains were starting to come out. That is why I continued repeating. I don't really remember how many times I repeated but it was several times over two or three days.
I also bought a new set of balls and use my old Centennials as a backup set. Someone noted that it is a good idea to change the set of balls after using for a few hours. In this way it is not necessary to stop and clean the balls after a few hours of use. Now I clean both sets the next day.
In addition I have learned that it is best to let a set of balls sit for 30 minutes (two hours is better) after cleaning. If you don't wait a bit the wax doesn't harden and you get some whithish spots in the balls from not so dry ball collisions.
Hope that helps.
BTW I suspect, but don't know, that most older sets of balls could be restored in this way. Anyone looking for a good cheap mechanical ball cleaner should see MrEightball. He sells them now and he posts here on the forum.