Do "Instance" Variables Work Across AppleScript to JXA?

Yes. It should work fine.
If you want help debugging, please upload your macro with both scripts, and highlight where you think it is not working.

However, you may want to use Local Variables instead of Instance Variables, unless you need to share the variables with a sub-macro.

But scripts can see both Local and Instance Variables.

You may want to read:
Tip: How Do I Get The Best Answer in the Shortest Time?

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