For the sake of discussion .... I'm gonna take your Dad's side.
Your Dad should not take the money out. Why? Losing that tax deferred status is a big deal. If Dad left the $50k in a tax deferrd acct invested in mutual funds that have a similar rate of return to the last 100 years .... it should double aprox every 7 or 8 years. He could live another 30 years so his money could double four times. Starting at $50k ....First, doubles to $100k .... Second, doubles to $200k, Third, doubles to $400k and Fourth doubles to $800k . Hmmm. That's starting to look like real money. : ) Tax deferred or Tax free compounded growth is no joke. If he were to take the money out, he just wouldn't make this kind of traction. Everytime he makes $100 , $50 goes to taxes.
Shannon: You have been doing well and your Dad has prob had fun watching you. ( I would) But, think about the experienced investors that post here. Candidly, 1 in 10 deals will be stinkers. Even if you do everything right. Squatters, insurance hikes, zoning changes, supply chain issues ..... No body is immune from this junk. How much of your Dad's retirement savings do you really want tied up in this? 10% ? 25% ?
I love self directed accounts but they are not going to be much help here. I love that you are taking action and learning. If Dad wants to move forward with the lending .... he could form his own business. Charge you points and fees and 12% or more. The "profit" goes in to his new Self Directed Solo 401k .... and he starts a new tax deferred account. But, we are getting a little paperwork heavy ...... If you are not afraid of the Lawyer/Accountant factor .... your Dad could partner with you on a deal with a lot of first year deapprectioation to offset some of the taxes from the 401k w/drawal.
It's time to get a really good accountant that loves strategy. Not a tax preparer. You want an accountant that specializes in small business / self employed. Take Dad. Have him/her run the numbers. Awesome investment in your future. Best of Luck!