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I've got to wipe my MacBook and reinstall all my applications fresh.
In Audition I have certain EQ / processing presets I've made myself I have saved. Also in Premiere Pro I have some transistion/codec settings saves
When I reinstall from Creative Cloud - will those presets still be there? Or is there a way I can make sure they're saved to the cloud?
If not, where do I find from my Time Machine back up?
No they don't. At least not by default.
All of that is local to your computer. You need to make Physical Backups of all your important files whether personal or ones you have created for the program you use.
Make a Note of where they came from, the PATH, and when restoring restore to that same PATH.