I THINK its in your best interest to file amended returns to record your depreciation and expenses. 

Wisconsin records are very open so most are already getting every single lead.

Also, I would not do some large change like add a bathroom or an addition that would change the particulars on the tax record. 

Don't forget to ensure you get all relevant records at close. 

If that amount is enough to pay you back with the interest, it may be worth you paying off his loan and doing a new, recorded loan on the property.If he is not getting a payoff amount to pay you off, you won't ever see the money.It may be better for you to buy the house for a fair price and rent it back to him.

Having spoken with a local title company they said all the liens judgements and data is done on line and we have access to the same records.

If this was willed to him, is there a record of his father/mother/relative who owned it before then?

Why not just take the hour to create the record. 

See also How to search eviction records for Wake County?

At the time it wasn't easy to find banks looking for young investors with little track record.