Sync is pretty buggy right now. Use at your own risk. Syncing of history can cause data loss if you delete a history item in one Opera. Syncing opened tabs can cause them to be separated into a different session (as seen on the opera://activity page) each time you start Opera. Syncing settings only supports certain settings, and as you've seen with workspaces, it might mess things up.
With that said, you can try starting all over to see if workspaces (not what's in them, but the workspaces themselves) will then sync correctly when choosing to sync settings. See https://forums.opera.com/post/289935 for how to start over with fresh profiles and fresh Opera Sync data. You'll have to recreate all your workspaces manually first. You'll then have to test if workspaces created in one Opera get added to the other Opera and vice versa instead of one Opera sacrificing its workspaces and accepting the other's. Opera might only support the latter. Guess it might be best to only set up workspaces in one Opera and then sync so the other Opera gets those workspaces (if that'll even work). For opened tabs, you'll have to back up and restore them as mentioned in the link or try syncing opened tabs, and if that alone doesn't work, goto the URL opera://activity, and open tabs from the other Opera in the workspace you want.