Without GST Invoice & Annual IT filings

I am providing repair/ renovation service to a construction company head office building. My service comes under Taxable GST service. Me and that particular company booth of them having GST number.

While I raised a GST Invoice on them for my repair/ renovation service. They where not accepting my Tax Invoice. Instead of that, they demanding without GST Invoice.

If I to do so, how I need to show that Invoice in my GST and annual retturn filings. Because from 2017-18 FY onwards the government implemented new rules, like the GST and Turnover in IT filings should not veary from one another.

My business still in growing stage. So, I don't like to loose that project for my further projects from that construction company and growth of my business.

So suggest me further what I need to do for this ?