If this is really true and he truly loved his son, he wouldn't have advised you to distribute shares for the investment instead of taking it on debt or heck something like a convertible debt.
Maybe the licencing deal will cost $100k/month, including consulting services from you to build the service, and unfortunately, it will turn out that the cloned CDBaby service is not profitable, and so it will be shut down after 33 months.
You'll still have to pay corporation tax on it (or whatever the equivalent is in the US), but hopefully that's less than trying to extract that money out of your dad's company.
Note: IANAA
His fathers business invested some money in his corporation. Now, from the story it appears that they didn't expect much of a return on this investment, but I don't think they acted predatory in any way.
I don't see why there should be any reason for a "payback" here, that is not how investing works, and quite frankly sounds very selfish and biased to me. If his business had completely failed and he ended up broke, would he be looking for a legal loophole to repay that $20,000 investment back to the company? I would tend to doubt it.
His scenario is almost exactly the model/concept of VC investing... Money is invested in seed companies knowing that it is highly probable it will be lost, but the slim chance of a large payoff makes the risk worthwhile.
The only reason I can think of without blaming his investor dad is his dad wants to shelter his kid all the time and doesn't think of him fit to run independently or doesn't want him to take that risk at all.
You could induce a period of low valuation to make a stock transfer though, thus costing less than the $3.3M.