@SuperOscar Well, worst case you can always delete the Web Data file from your profile dir. It will regenerate the search engines from scratch. Unfortunately this will also delete your autofill data, saved addresses and credit cards if you have saved those.

However, it's possible that with Sync enabled the redundant entries from another device will just sync back.

I don't know how technical you are but the Web Data file is just a SQLite database. You can use the sqlite3 tool to query it, and even delete rows (although doing so is not really "supported"):
https://www.sqlite.org/cli.html

Obviously any changes to the database will have to be done while the browser is closed, as the file is locked.

These are the default engines for my locale (Norwegian):

The sync_guid is what sync uses to decide if something is a duplicate. It should be unique for each engine. If it's different then you'll get duplicates because Sync will think it's a different engine.

Possibility to import/export Site Authorization settings?