Google manual submissions

That sounds unfortunate ...

Hard to say exactly why the site would have fallen, but continual resubmission is nonsense in my view. Once in the index you're in the index, and Google has a process for deleting any duplicate versions of your page that might slip through.

The sudden appearance of 1000s of (possibly not that relevant) backlinks won't do you any ranking favours either. Google is monitoring your "Linking Profile" and a step change like this may raise an alarm as it's unlikely to happen because of  "natural" linking to good quality content etc and they'll see it as the sort of spamming tactic that it probably is.

Sounds like you were doing a good job before; nothing beats long term commitment to developing good quality content.

Good luck convincing your boss!