Short answer is no - the only time you should ever delete these values is if a mistake has been made. You should never delete or edit them simply to make a time off balance calculate correctly.
Why? The main reason is that the values for time off in lieu are cumulative.
For example, Joe Bloggs has 5 hours TOIL - he takes those hours, the system has 5 hours TOIL recorded and his balances are correct.
He then gets another 5 hours TOIL but you decide to delete his previous 5 hours - once you do this he still has 5 hours TOIL booked but he now has no allowance. As a result, his TOIL balance will be 0 and not the 5 he is entitled to.
If you find an obvious error in time off in lieu then you can delete the values - for example someone with an incorrect time off in lieu value due to a mistake in a timesheet. Under any other circumstances, you should leave all time off in lieu values in situ.