We never needed it as all our styles fit perfectly into each sub-account, but if I needed to do it, I'd use JS to differentiate between courses. So basically, you'd define your CSS classes as normal and then use JS to apply to them to only one course. As each course has a unique identifier in the URL (the number in https://danes.instructure.com/courses/204 , for example) and we know these numbers before writing the script, you'd just have to refer to them and use an if-statement to differentiate.
This will require some coding skills and some time to write and test, though.
If the course 1 identifier is 204 and the course 2 identifier is 209, and you want course 1 to be styled and course 2 not to be, the progress and code would be something like:
> Upload a normal stylesheet that defines everything you want for course one (204)
> In JS, write a function that searches the current URL for the identifier number and have it return this as a global variable (this may be helpful Get the current URL with JavaScript? - Stack Overflow)
> Write a JS if-function to check if 209 (course 2, un-styled) is present in the current URL (using the variable from the previous function for comparison)
> If true, use JS to revert your style changes back to the original (see how to alter CSS in JS here JavaScript DOM CSS)
> Both functions in JS have to be called every time the user loads a page in the entire account/sub-account.
> If you're getting really into it, you could also try to use jQuery to make sure the functions fire before anything else is visually loaded using something like $( document ).ready(){} https://learn.jquery.com/using-jquery-core/document-ready/
> Upload both the JavaScript document and the CSS document to the account/sub-account.
This is all theoretical, but if you have the coding skills or an IT guy/web-designer at hand, you could probably pull it off.
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