If a Will was probated in the county that the deceased lived but they owned property in another county, does it have to be probated in both counties?

I am so sorry for your loss.  You are correct that the Will is probate in the county in which the deceent resided at the time of their death.  If the other property is in the same state then it is all covered under one probate proceeding.  It is only if the property is located in another state that an ancillary probate is done.  Good luck.