1. For Gmail and Microsoft Exchange / Office 365 accounts, email threading is handled by the provider. Nylas only sync the messages and thread information attached to them. If it is happening frequently, please reach out to the users' email admin.
If the threaded view on the provider is different than what is returned from Nylas, please create a support ticket for us to investigate further.
2. For IMAP accounts only, Nylas handles email threading. Please create a support ticket for us to investigate further.
PS: For threading to work, the subject of the response has to be the same as the original message. If the subject changes, the response won't be threaded with the original email.