Robert, I believe there is a brief window [ possibly 2 years, but then again the surface owner may not have completed that step at all ] between the time that the surface owner succeeds to the mineral interests, granted by the court, and the time that they can return to the court and perfect their title, at which point, nobody can successfully challenge the landowners title. I think the period is 2 years.
I have not personally been through this. I have helped people with what to do before the surface owner who was making the attempt to succeed to their interest did so.
I hate to say it but I think you need the help of a lawyer just to decide if there is anything that can be done, due to the amount of time that has passed.
If the surface owner never went back to court to perfect their title, it's possible [ if too much time has not passed ] to challenge the surface owners title and if you win you will have to reimburse their fees legal and probably otherwise. The surface owner may have already leased the minerals and received bonus and possibly royalty from any wells that have been drilled, even if you win that is gone, the surface owner gets to keep that according to my understanding. The lease will still stand because the surface owner was legally entitled to lease the minerals at the time they did so, once again, assuming you win.
Robert, I would sit down and do a cold calculated cost benefit analysis. It might cost you $50,000 to regain your mineral rights, after the bonus and possibly some of the best royalty is already gone. If you had 10 net acres and won, you might break even in 20-40 years, in that case I would suggest that you invest the $50,000 in a pipeline company or something. If you had 20 net acres I would keep in mind that I probably wouldn't regain my expenses for 10 years. If you would recover 40 net acres, I would say that it would probably be worth doing, after finding a lawyer who genuinely agreed that it was a good idea, and not just because it's billable hours.
I would make haste slowly before you start a bottomless pit of legal fees with a lawyer's aid doing research. You could get an NDRIN Recorders Network subscription for $25. They take credit cards. You would be able to check the records to see if the surface owner had perfected title to the mineral estate, before you started talking to the expensive lawyer. When doing the search I suggest you search for every single document filed in the section that contained your mineral acres, searching by document title or exact legal descriptions has missed documents for me before and an extra hour of yours or my time is a lot cheaper than a lawyers time. This is the best I have for you with what you have told us. I hope it helps.