Well, it's exactly like that. There's only PID, Moves, Species, HeldItem, Level and EVs (not per stat, only one value that's applied to each stat).
PKHeX already has the data structure, it's just missing a GUI.
Start a new save and import the Gen 5 Living Dex pcdata.bin from here. It has all Pokemon but on different levels.
Alternatively you could use the ALM plugin and generate your own Living Dex mons. All will be level 100.
https://github.com/santacrab2/PKHeX-Plugins/releases/latest
The latest version of the plugin (2.2.2) should work fine on the latest version of PKHeX (24.03.26).
The plugins folder has to be next to the PKHeX.exe, so like this:
The plugin also won't show up if you don't have a save loaded.
The file is full of garbage, no real save data inside.
Besides that the proper size for Gen 3 saves is 128kb. You should check if FlashGBX is able to dump the full 128kb save.
He provided ME3 files for them on his Github https://github.com/notblisy/RUBYSAPPHIREDLC/tree/main/MYSTERY EVENT 3 EVENTS
Use the WC3 Plugin to inject them into your save.
No, you can still use the file and you don't have to delete anything.
Your .nds file can not just disappear after using PKHeX. PKHeX does not remove or delete files. It still has to be somewhere.