Is it possible to use different versions of same language with different prefixes? I am building a multi language website. I would like to use 2 instances of same language (maybe with slightly different translations).

So is it somehow possible to use different versions of same language with different prefixes?
Yes you can.

Go to the languages settings page (admin/config/regional/language) and click on the Add Language link.

There you can select a preexisting language, but below of that list is a Custom Language option.

Fill that form with your new language settings and there you have your new language.

To start, I'd suggest to export (admin/config/regional/translate/export) your main language and import it (admin/config/regional/translate/import) in your new language. It will give you a translated new language. Then, you can go to the translate interface and update the texts that must be different.