Final Settlement Process after maternity leave - salary was made proportional to her working hours

Hello, I am looking for some guidance and suggestion in the below given matter.

One of our Employee Resigned soon after coming from Maternity Leave (technically we gave 1 month extension post her maternity leave). We also offered her WFH, flexible hours , on need basis logging in office but some how things did not work out from resource end and she resigned. So as per the term of notice period she served notice period but with limited hours login , i.e instead of 9 hours she logged in for 4-5 hours in a day. We had a clear instruction and guidelines given to her to have clean attendance record and login maintained but, it was one difficult resource.

The point is she served notice with limited hours of contribution and left. Her salary was made propotional to her working hours for the first and second month (i.e if she has worked 5 hours a day, the salary paid was those 5 hours) , the final month was kept for FNF. Now during the FNF the management has suggested to recover salary for the shortfall of hours i.e she has made contribution and i need help in this matter.

a. Originally it is 9 hours per day (Inclusive of break hours) and her Contribution is 5 hours(inclusive of break).

b. Salary made is only for 5 hours per day.

c. Remaining 4 hours the suggestion is to recover from the 5 hours(i.e from point "b") can we do this?

Is the above a valid thought?

I think that the individual is a monthly rated salary employee with a 9-hour work schedule per day including rest interval. The fact that she was allowed WFH shows that the establishment would be one coming under the Shops and Establishments Act though the post does not convey this. It is also not clear whether the work schedule is that of 5-day week or 6-day week and the paid weekly holiday is one day or two days. In any case the normal working hours per week shall not exceed 48 hours in total.
Post her leave, she has worked for 3 months in total and the third month was the notice period. For the first two months she was paid salary proportionate to the actual hours she worked. During the the third month also she continued to work for only 5 hours a day in stead of 9 hours. Had she bought out the notice period in stead of actually working, she would have to pay for the entire month's salary.
Therefore, it seems correct to me to effect recovery for the unserved notice period from the salary payable for the actual period worked.

Thank you for your response Mr. Umakanthan.