If your ancestor owned property in more than one county in the same state, there probably was just one probate case. That case was likely in the county where the bulk of the property was located. If your ancestor’s farm was split in two counties, the same is probably true–where the bulk of the real estate was situated.
If your ancestor owned real property in two states, there probate was likely done where he lived or most of his property was owned.
It is possible that the estate was probated in both states, perhaps at different points in time. This can happen if property in another state is discovered after the estate in the original state has been closed.