My first contact with BP was an old kit gun ( wish I could remember what company) with this same problem. I think the cylinder bolt slots were cut wrong. I traded it for another pistol with one scarred cylinder cavity. I know that doesn't help, but I gave up on it.
At the time I knew nothing about BP pistols (probably still don't
). First you should try another cylinder if you can, to see if it's your cylinder. If you have a Cabelas close, you could take your Remmie in, to see if one of their spare cylinders would fix it ($50). Or if you had a friend with a Remmie to let you check fit.
I sanded a wooden dowel down to just snugly fit through the barrel and into a cylinder cavity. Then I noted how far off the cylinder bolt fit was for each cavity. This will tell you if the bolt slots are consistant around the cylinder.
If they are consistant and you don't think it's the cylinder, or can't try a different one, or just want to make that one work....whew....then you are left with modifying the bolt to get it in time. This might involve adding metal to one side and removing it from the other, then heat treating if you like. Remember the bolt still needs to fit through the slot in the frame, so you might need to change that, And it would be nice to have a close fit there to help steady the bolt.
It comes down to how much work you think it needs. I am disappointed that Pietta let that one slip. How old is it (date code)?
It would also be nice to compare your bolt to another Remmie in case you could just change a bad bolt. Hope this helps. Maybe others will have better solutions.