Note this isn't the only correct way to do things, but it's what I'd do to avoid excessive dropbox syncing, and a slim chance of sync issues.
- Go ahead and download Scrivener 3. You can install it if you want, but don't open any of your iOS-synced projects yet.
- If you have changes from the iOS version pending, sync those from your iOS devices.
- Pause Dropbox on your Mac after it's had time to sync any recent changes from other devices.
- Open each project in Scrivener 3. This will rename your original project to include "backup" or something like that in its name, then it will create a new version of the project that is compatible with Scrivener 3.
- Move the backups of the version 2 projects out of the folder that syncs with the iOS version. I suggest that you remove it from the dropbox folder and into your Scrivener backups folder, just to save time during the next step…
- Re-enable dropbox, and let it complete the syncing process.
- (optionally, close your projects in Scrivener for Mac, and then…) open Scrivener for iOS and sync all your new, scrivener 3-compatible projects.
That should do it! Hopefully, that's helpful to a couple of people.
Edited to add step to sync from iOS devices, in case anyone forgets to check that.