I found a case decided by Gujarat High court, which says there is no need to deduct PF if the amount is paid as compensation.
In Swastik Textile Engineers Pvt. Ltd. Vs. Virjibhai Mavjibhai Rathod and Anr., Guj, 2007
It was held that
Service - Contribution amount of back wages - Order passed to make provident fund contribution in respect of amount of back wages paid to the Respondent No. 1 - workman under challenge - Held, Court awards back wages for the period employee was kept away from duty, what the Court does was to award damages assessed in terms of whole or part of the wages the workman would have earned had he continued in service without interruption - It was not the same as payment of wages for duties performed or for period deemed to had spent on duty - Amount of damages or compensation awarded by a Court would not constitute Amount of back wages paid to workman did not constitute the 'basic wages'.
The judge opined that
12. In my view, when the Court awards backwages for the period the employee was kept away from duty, what the Court does is to award damages assessed in terms of whole or part of the wages the workman would have earned had he been continued in service without interruption. It is not the same as payment of wages for the duties performed or for the period deemed to have been spent on duty. The amount of damages or the compensation awarded by a Court would not constitute the 'basic wages' as envisaged by the Act.
13. For the aforesaid reasons, I am of the opinion that the amount of backwages paid to the workman did not constitute the 'basic wages' as envisaged by the Act. The petitioner, was therefore, under no obligation to make statutory contribution to the provident fund under the Act.
VIJAY