S Corp owner gets SBA loan. (I have not seen the loan documents but I assume are in the name of the corporation).  It is apparent that she used those funds to build a personal residence and to invest in stocks personally.  Any CYA needed on my part?

The large SBA Loan Liability and the related SH Loan receivable on the Balance Sheet seem like an invitation to audit. 

I have advised her to create a loan document, sign it, and repay it in equal installments with interest at the AFR.