Design the big data with mongo db
If the files are sorted you can just find the id or timestamp of the last inserted document in the database, then only insert the records in the files which have ids that come after that id.

If they are sorted by _id or timestamp then doing this should be trivial.

The solutions you came up with are great as well.

However, be aware that creating entirely new collections will be slower than what i proposed, and upserting will be even slower than that.