Yeah I triple checked I wasn't making any of those mistakes. The save file is called sav.dat, does that have anything to do with it? Because PKHeX reads it anyway... Still when I inject the save and reload the game none of my edits appear.
PKHeX works fine for me with those games, even the rom hacks like Pokemon Brown. I'm not sure what you're doing wrong but it sounds like, you're either not overwriting the save before replacing it, you're replacing the old one, or it's not overwriting the old one when you put it on your SD card. Save.dat is the proper file for those saves. My advice would be to do this:
1. Export the save to SD
2. Copy "save.dat" to desktop
3. Delete the "sav.dat" on your SD card
4. Edit the save from the desktop in PKHeX
5. Export the save from PKHeX to your desktop, let it overwrite the old one.
6. Close PKHeX, then load your edited save to check for your edits.
7. If present, copy the save to your SD card ( You deleted the old one, so no chance of it not overwriting properly)
8. Load Pokemon Red Deluxe, and save the game.
9. Delete the Secure Data Value in SDF
10. Import your save.
11. Profit??
Alternatively you can try a different save manager. I recommend JKSV, it works on all those games and deletes the secure value automatically. Not to mention it uses the actual Title of the game instead of the ID# when you're choosing so there is no room for error.
I would also like to point out that the Title ID of Pokemon Red Deluxe
IS NOT the same as Pokemon Red. So if you used a tutorial or something to get the Title ID to use with SDF, you're replacing the wrong save.