1) User requests account deletion. Facebook does not delete it, keeps track of his phone number via shadow profiles. (Mike is still mike@gmail.com, 800-555-1234)
2) User creates a new Proton Mail address. (Fakey@protonmail.com)
3) One of his friends adds that email address to his contact. (Mike, mike@gmail.com, fakey@protonmail.com, 800-555-1234). This user is on Instagram, Facebook, or has some mobile app that uses their analytics.
4) Facebook makes the association after scraping his friends contact list.
Essentially, his friends betrayed him, likely unintentionally.