How do you archive, deduplicate and search e-mails offline?

I have thousands of emails from multiple accounts. Some of them are .eml and others are entire .mbox mailboxes.

I would like to be able to search them and also import new emails (manually, I'm not going to connect to IMAP or anything else). It would need to ignore duplicated e-mails e.g. re-import a Google Takeout .mbox without creating complete chaos.

- me@example.com -- inbox -- sent -- folder1 -- folder2

- the-other-me@example.com -- inbox -- sent -- thingsishouldnthavesent