Hi - I've been struggling with this too, and going round and round with QBO support. No guarantee this is correct - but I think it is:

Delete the entry generated by bringing in the deposit from your bank in the chart of account loan account.

Open the journal entry made in the chart of account and click 'EDIT'

  Line 1. I had a GROSS amount of the loan (example $1,000.00) entered as a CREDIT.

  Line 2. The deposit from the bank was a NET amount (example $900.00) entered as a DEBIT.

  Line 3. The UCC filing fee the SBA deducted (example $100.00) entered as a DEBIT.

I now have a $900 deposit in my checking account.

An expense of $100 for the UCC Filing fee

A chart of account loan showing $1,000.

I'd love any feedback if anyone knows this is correct or not.

Thanks - Pam