Considerations for Leave Payment and Allowances
That depends on the way your company views leave payment. If they consider allowances as part of the salary structure or for convenience, then they will proportionately deduct all allowances, including conveyance allowance.
It is a small part of your salary, so it's best not to make too much noise about it.
While an employee has come and gone, her conveyance cost remains the same. Most employers will deduct half the amount. In an extreme case, consider if the employee came to work and left after an hour for personal reasons. Will the company pay her conveyance allowance for a day?