Atmosphere take care of that.
On Atmosphère 1.5.1 A feature was added to optionally mirror the bluetooth pairing database to the SD card (thanks
@ndeadly). This allows device pairings to be automatically kept in-sync across sysmmc/all emummcs.
This is opt-in, and can be controlled by setting: atmosphere!enable_external_bluetooth_db = u8!0x1.
When enabled, the pairing database will be synchronized to /atmosphere/bluetooth_devices.db.
You need modify the file "atmosphere/config/system_settings.ini"
Then on the section
[atmosphere]
Change the value
enable_external_bluetooth_db
For:
enable_external_bluetooth_db = u8!0x1
More information on:
https://gbatemp.net/threads/pairing-the-joy-con-on-emunand-and-sysnand.562519/post-10461487