Bit confused about when you recommended to initialize the source PS4 and that this deactivates all accounts. Does it deactivate the PS4 because to deactivate a PS4 I thought you had to go here:
http://manuals.playstation.net/document/en/ps4/settings/activation.html
Whereas for initializing, the manual does not specifically say whether the actual PS4 is deactivated as the primary:
http://manuals.playstation.net/document/en/ps4/settings/restore_system.html
So, before I trade mine in I will:
1. Make sure I am signed into the PS4 (including sub accounts)
2. Just in case, backup all user data to a USB
http://manuals.playstation.net/document/en/ps4/settings/data_system.html
3. Sync trophies just in case
4. Remove any easy to reinstall games I have physical versions of, eg Titanfall 2 at this time of writing had an 80mb patch only. Delete all physically owned games that have minimal install requirements. Saves a lot of wasted time on backup/restore
4. Backup my 2tb PS4 to an external 2tb USB attached drive
5. Now deactivate my PS4
6. Put original 500gb back in the to be traded PS4 which will cause it to initialize. Do not sign into PSN
7. Get PS4 Pro, put my 2tb 2.5in hdd in before turning on.
8. Have the 900mb System Restore handy on USB and have PS4 Pro set to go (make sure system software is same version)
9. Sign into new PS4 Pro and activate as primary
10. Perform restore from external 2tb HDD