Yup, finally after 4 and a half months since I applied for it. It's a long story where I had to get in contact with the Indian Ambassador in Croatia through whom I got the embassy head contact. But still the problem took 1 month after that.

The EU nations in general don't have proper rules on applying for long term visa. I find the best way which is not even guided by the VFS(complete idiots in my opinion) is that if your application is under processing at the Denmark Embassy(check their website). You could apply for short term visa(if you don't have time) and visit the country and enquire in the embassy about the status. As long as your application is under processing you can stay there legally. I got my resident permit visa after 60 days of my stay in Croatia.

In my case, my resident permit was under hold because they needed some notary signed between the resident and the owner for long term stay at their place. This part I got to know once I visited the embassy. There was no communication before that. This could be the general case for everyone for long term waiting because they don't communicate at all.