I submitted a confirmed flight reservation with my visa application a few days ago and when I checked the flight today, I realized that it was automatically cancelled.
Will this have a negative affect on the result of my application? What can I do to fix this issue?
From your wording, it appears you made an unpaid reservation on the airline which is held for a period of time during which payment must be made or the reservation is automatically voided.
American Airlines for example has that option.
Courtesy of Gayot Fow and multiple anecdotal sources, UK doesn’t care and there is no issue to fix. It will not have an effect on this or future applications. Exogenous events like what you described do not affect the decision process; and they are specific that flight reservations are not required for visa applications in the first instance.
From the Visitor Supporting Documents Checklist only transit visas require a booked/confirmed ticket.