Can the money taken from the company be returned due to my failure to submit my annual flight ticket invoices, and would this be considered a repayment of the money?

If you have a fixed right to the ticket price from the company, and you forgo this right in exchange for the money you took from them, as you found no other direct way, then we hope that this will suffice as a repayment of the funds to them, provided that the ticket price is not less than the money you took.