Yes, that goes without saying as I first recommended in post #2 (although maybe I wasn't entirely clear, that happens sometimes -- I spend later posts explaining what I implied in earlier posts
).
But you did ask for "any ideas on how to automate a sync-up between an empty and non-empty library?" -- emphasis on the
automate.
Automation suggests things like include/exclude patterns for your sync software (ideally has a command-line method of invocation), followed by scripted callibredb commands to "heal" the database.