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1) This document explains the submission of invoice in electronic format AT customer’s server

2) This document explains the submission of invoice in electronic format IN customer’s server

3) This document explains the submission of invoice in electronic format ON customer’s server
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I would have said 'submission to' or 'through'. I presume that the invoice is being submitted to the customer, as are normal paper invoices, but here it's done through/via the internet server. But if those are the only 3 choices, then I'll choose 'on a server'.
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I would write:

This document explains how to submit invoices to the customer's server in electronic format.

Emotion: smile