What is the Sharia ruling on preparing papers for requesting bank guarantees with cash cover and commission, and would I be committing a sin by doing so, given that it is not my primary job?

A bank guarantee may be permissible or impermissible. It is not permissible to charge a fee for the guarantee itself. However, it is permissible to charge for administrative expenses and for the actual services rendered in issuing the letter, provided that these charges do not exceed the customary fee (ajr al-mithl). It is not permissible to issue a letter of guarantee to someone who requests it for the purpose of obtaining an interest-based loan (riba) or for an impermissible transaction. Your work in recording these transactions is permissible, and your wages are lawful if the bank charges only the actual expenses without excess. Otherwise, it is not permissible for you to work on their completion.