They are independent in the sense the sync data belongs to each location and is not shared or transferred to other locations, including different sync methods. So there is no prep work that needs to happen in DEVONthink before switching to a new sync method.
However, if you’re going to stop using CloudKit, I would suggest you Control-click the sync location, and choose Clean Location first. This will remove the sync data and free up space in your iCloud account. Then set up Bonjour. I’d suggest this page as a reference…