Amendments to income tax

Hello Experts,

My question is regarding Amendments to Income Tax return. 

I am into software and was deputed to onsite by a software company. While sending onsite, company asked me to sign on letter of assignment in which one of the condition was to that any tax refund which is for that period I work onsite, will go to the company.

Subsequently, the company is filling an amendment to my tax return where in the refund amount will go to the software company.

I would like to know if this is legal? What if I do not wish to file the amendment?

Thanks in advance.