This will usually affect an employee who falls under ESI and PF. Consider an employee with the following custom salary structure -

Now, let's say we need to put a deduction of Rs 5000 to this month's payroll. The gross pay, thus, needs to be 17960-5000 = 12960.

How do we accomplish this? A simple way to think about it would be to just remove Rs 5000 from the regular components like special allowance, HRA, and basic salary -

However, if we do this, then our ESI and PF employer contributions will be incorrect, since these are calculated as a percentage of other components (to see how PF and ESI are calculated, please refer to our FAQs here and here). What needs to be done is that all the components need to be lowered just enough that with the updated PF and ESI values, the gross pay comes out correct. On top of this, there can be added complications of unknown or missing components as well. Overall, this is a problem that cannot be reliably solved using pure math. Hence, in such cases XPayroll removed the custom salary structure, and assigns a new structure which it back-calculates from the required gross pay.