I have a small gear pump that has viton seals. Will the seals be damaged if I pump Atlas Copco synthetic oil through it?

Have no idea. Is Copco an ester or PAO? Also there are different Vitons. In addition to basestock you have to worry about additives whose effect can be counter intuitive. Best way to get an initial feel is to cut a viton seal into two - submerge one piece of the viton seal in the oil at the expected operating temperature. After a few days, pull out seal and wipe off with white cloth. Anything come off on cloth? Look to see if submerged seal has different appearance (color, swell, shrinkage) or feel (softer or harder) compared to other piece. Would think manufacturere of Atlas Copco has some literature with compatibility charts.