I've found a marginal fix that's probably good enough: when reimporting don't delete your atlas or data files, but DO delete all of the old textures it imported. That's what triggers the replacement dialogue. If you get rid of them first then you won't get any warnings importing the rest of it. Then only re-import the JSON file and it'll re-fetch everything it needs.
The other benefit to this is you won't need to restore the hard references to your spine assets in your actors, they'll stay as they were.
I'll add a button to the utility script I've been setting up to delete all of the images associated with the selected atlas, should make it a bit easier to find them if you're only reimporting selectively.
