well, I didn't make a backup. I was desperate to fix this video issue with my system, and I didn't really care if I lost everything. don't even play the system, haven't progressed in any game ever since I exploited it several years ago, and I've never even started a pirated game. I'm glad I did it this way though, because now I understand how the databases are tied together.@godreborn A way to avoid all that is to make a backup of your profile using the official backup/resore in system settings before you change the HDD or initialise the PS4 and then restore that backup after you have installed the new HDD.
Doing this will make all internal ID's the same so that any databases, saves, trophy files etc. will be compatable straight away..