That is just too many notes for a single project, I’m afraid. I think you would be best to try to export notes from Evernote in groups, if possible. Perhaps 100 notes at a time.
Note that Agenda is quite a different type of app to Evernote. It is probably not ideal for that many notes. It is not designed as a place to drop lots of data. It has a special time based structure, which makes it more suitable as a way to work through projects etc. The best solution may end up being Evernote for a dropbox of stuff, with Agenda for project management.