The authority that rejected your claim for TED refund has clearly not understood the nature and purpose of the Cenvat credit scheme.
In effect, the scheme gives back the excise duty on inputs used, so that this does not inflate the value for terminal excise duty, and so that terminal excise duty is levied on the product value only and not on the tax portion of its input cost. The 'giving back' is in the form of a 'Cenvat credit', which is used like cash to pay excise duty on the final (terminal) product. The fact that terminal excise duty on the capital goods has been paid out of Cenvat credit does not take away their duty-paid nature.