"and repayments of contributions can be just distributions"

You already told us the loan(s) won't be repaid: "he advanced the company $50,000 and will never be repaid."

Now there are funds available?

"There are no written notes. These are just advances to the company when they need money."

Or, capital infusions. In other words, money in and money out isn't Debt unless it's structured as such.

The real issue is, you seem to want to write it off as a loss: "take short term capital loss as a non business bad debt."

You also told us: "Through the years"

Unless you can straighten out this story and stand behind it formally as Debt, you should consider what it would look like if it is examined. Because from here, so far, it looks like capital from the Shareholder, and distributions to the shareholder. Not debt from one or more notes payable, interest and principal.