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This really depends on the rules that have been established by the contractor. So, you need to check the contractor's rules. If the rules have been violated, you can file complaint against the contractor with the federal agency that awarded the contract to the contractor.
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Phillips' response was 100% correct. There is nothing that would legally prevent this company from not giving you a 100% per diem, so this situation would be governed solely by the internal policies of the contractor and any contract you have with them.