There's a difference in Affinity Photo between saving and exporting.
Suppose you launch Affinity Photo and use it to Open a picture using the file browser dialog, (which also displays the Apple media browser of images within Apple Photos - and iPhoto if you're still using it).
When you edit the image (say a file called Pic1.jpg) using Affinity Photo, and then Save or Save As... it will save an Affinity-only version of the file called Pic1.afphoto, which retains all the extra information about non-destructive editing changes, adjustments, layers, saved selections, clipping masks etc etc etc. This file can only be opened and viewed using Affinity Photo, and the adjustments will still be accessible.
But if you want to use the edited image for another purpose (email, graphics program, web, iPhoto, Apple Photos...) then you have to Export it from Affinity Photo in a more generic format such as .jpg, .tiff, .png. Exported files can be viewed, opened and edited on Macs and PCs using standard software and imported into Apple Photos and iPhoto.
When you export the image, your original Pic1.jpg stays where it was when you opened it and remains unchanged. This is why opening and editing a picture using Affinity Photo via the Apple media browser doesn't update the original in Apple Photos. You can't do a "round trip", as it's sometimes called.
It doesn't matter where you keep your iPhoto or Apple Photos library, or how big your external hard disk is - the same principles apply:
If you want get an edited version of the picture into Apple Photos, or iPhoto, then you Open, edit and Export using Affinity Photo. This gives you a flattened copy (.jpg, .tiff, png...), in the folder of your choice, that you can then Import into Apple Photos or iPhoto, or send in an email, or upload to a web server.
Photoshop can save and edit in different formats. But even in Photoshop, if you try to save a document with layers, clipping masks, vector objects etc as a .jpg or .eps, you will still be forced to save it as a flattened copy, which is the same principle as Affinity Photo's Export.