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Yes, I moved all my journal notes into a dedicated “Journal” folder shortly after setup before linking (while all other notes remained in the iCloud folder), and that didn’t affect anything.
I’ve also moved some newer notes – like recipe notes – after I had already added links and marked them, and that didn’t cause any issues either.
So based on my experience, moving notes to other folders after setup and linking hasn’t disrupted anything.
That said, I’d suggest trying it with just one note first, to see how it works for you, before moving everything.