This is case where you need to see a good experienced solicitor, as it raises the complex issue of Adverse Possession.
If your uncle had adverse possession of the land (i.e. held it for at least 12 years unchallenged and without paying rent etc) then it is likely that ALL of the land forms part of his estate.
Technically, you will end up with the same "ownership" result, i.e. your father and your uncle should receive 50% each. However, the CAT implications will be different.
If the farm was above the relevant Capital acquisitions Tax threshold the estate might have a legacy CAT liability.
Jim Stafford