unpaid allowances for food, accomodation and local conveyance

i would like to consult my scenario in which it has recently come to my attention that my contract with our company states that i should have been working in visayas as my base location but i have been working in manila for almost four(4) years. This issue arised when a sudden transfer contract was asked of us to sign stating that the company will be transferring us to distant provinces where our only option is either to sign that i agree or not agree to the transfer which also states that there will not be any allowances provided only our regular pay. having seen the contract, i asked the people in charge about the sudden transfer where in they replied that it is their right to transfer us as needed by the project as stated on our contract.

my question is if they say that everything is as per contract then shouldnt they pay allowances that were not given to me for having been working in manila, or so to say deployed in another location outside of my base location as per contract?

hoping to hear from you guys soon. thanks/