Hope you want doing good.

You have elaborated your question quite nicely but you failed to mention about the exam you are talking about.

Different counselling authorities have different guidelines about erefunds  and upgradation.

I don't know which exam you are talking about.

For example, when I was applying for state counselling of Odisha last year, the the fees can only be refunded within a limited time period. If you fail to apply for it you would miss the chance. most other counselling authority's follow the same guidelines.

Yes the upgradation fee would be for every other counselling stage. You don't need to pay upgradation fee for each round of counselling.

If you have any more doubts you can ask them in the comment section and also please mention the exam you are talking about in the comment section I would be more than happy to help you.