I had the same issue, I submitted my application yesterday and hope what I have done is ok.
I bank with Santander UK. I requested a reference letter around 2 weeks ago and once received it did not meet CIC requirements. After speaking with Santander they advised they cannot amend the standard letter. I asked them to confirm this in writing. I went to the branch and asked them to print and certify 6 month bank statements (as I understand CIC do not accept online statements).
In my application, I uploaded the certified bank statements, the reference letter, the letter confirming they cannot make changes to the reference letter, and a letter of explanation. Hopefully this is ok as there was nothing else I was able to obtain!