1099 R question

We took a distribution in Feb last year to loan my son some money for his new home. The money came from my husbands IRA. The bank broker sold some mutual funds from the IRA account. My son paid us back, but not within 60 days, it was closer to 90 days. We put most of the money back into the same IRA plus our brokerage account. 

My question is... since the mutual funds were not performing very well over the years and were considered a long term investment, must we pay taxes on the full amount of the distribution or can we adjust the amount to come up with a cost basis? I've always used TT to do my taxes, this year I'm freaking out that I may have to include the full $55,000 as taxable income. Please Help!!!