Firstly, if you stand to lose a lot of money based on this it would be worthwhile taking advice as the answer will depend on the exact wording contained in pre-contract correspondence. As such it's difficult to give a view based on the limited information you've provided.
In a general sense, the act of amending and returning the subcontract could be seen to be a counter-offer, unless you had already commenced work before it was returned, in which case your actions could be seen as acceptance of the terms proposed by the contractor. If you hadn't commenced work before returning the amended terms then the act of payment or absence of a further counter-offer by the contractor could be seen as acceptance of your counter-offer.
In a general sense, the act of amending and returning the subcontract could be seen to be a counter-offer, unless you had already commenced work before it was returned, in which case your actions could be seen as acceptance of the terms proposed by the contractor. If you hadn't commenced work before returning the amended terms then the act of payment or absence of a further counter-offer by the contractor could be seen as acceptance of your counter-offer.