Eh? No idea how you might have got there, that's quite a leap in the wrong direction!
All you need to do in your JIRA is separate out the schemes. Let's say you have the default scheme and it's called permissions-A. If you want to make project ABC work differently to project DEF, then you change the schemes for them. Create a new permission scheme called permissions-B, set it up the way you need it and associate it with the DEF.
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