If the jest is kept, why isn't it "twoją sprawą"?
Because the subject is the dummy pronoun "to" and in such a situation you just use Nominative.
To jest nie twoja sprawa. What is wrong?
I guess it's also a possibility. Added now.
The nuances are different: "to nie jest twoja sprawa" is a bit like "this isn't + your business" while "to jest nie twoja sprawa" like "this is + not your business".
So what's the difference? Does the 2nd version add some emphasis on "your"?
I read it as "this is someone else's business". It's correct, but I'd consider it odd.