Blackjewel LLC took more than $52.8 million in loans from its former chairman and chief executive, most of which the business repaid, in the six months before the coal-mining company’s sudden bankruptcy, which has left workers unpaid and the future of some of its mines uncertain.

Loans from Blackjewel’s former chief executive officer and president, Jeff Hoops Sr., were the source of a dispute between the coal business and senior lender Riverstone Credit Partners that the company has said was the cause of its chapter 11 filing....