Let me summarise the facts and issues as I understand from your statements:
The Indian company builds machines with the parts, for which the payments are made by you and these machines produce specific bottle caps exclusively for your customers. These bottle caps are exported to you.
The Indian company faces problem with its banks/local authorities, when the money is received from you, as the machines do not leave the country and hence, they are not treated as "export" of goods.
Why is that there is problem when the money is received from you with the bank/local authorities? Is there no "export" of goods when the machines do not leave the country?
I restated the facts and issues to bring out clarity in respect of statements made by you. I hope the restated facts and issues are properly representing your statements and problems.
Now my views on the issues:
There are two kinds of payments from you to the Indian party, the first one is for the payment towards "parts" for building the machines in their factory. The machines and the caps are specific to your requirements. In this case the ownership of the machines depends upon your agreement specifically. However, when the payments are made by you for the "parts", which seems to be sourced by the Indian party with its own efforts, there is no acquisition of the machines by you. Hence I do not think the ownership of the machines vest with you, though they are specifically used for your products. There is no element of export of goods or services, when you are making payment for "parts", unless such payment is treated as advance for purchase of caps.
The second payment by you is towards export of bottle caps. Here, I don't think there should be any problem in treating this as "export" and it is nothing to do with the machines but I presume that there is movement of bottle caps from India to your country.