If you leave got removed in the leave module when approved in the eportal, then there may be a missing setting in the leave policy. Usually, this is caused by the costing method in the leave policy. Please check as follows:
Go to the Leave module.
Click Setup and select Leave Policy.
Check the Leave Policy if a costing method is defined other than TWWDays.
Click Costing Method in the Leave Policy.
Check if the employee Category, Position, or Department is missing.
Add the missing field and click Save.
Go to Process Leave and Initialise the employee again.