Trying to edit my Sapphire save but it acts weirdly?

[WitchDianna]

I made a dump of my Sapphire's save file with a Joey Jr. I loaded it up in mGBA to make sure everything is ok, and I opened the .sav in PKHeX to add 2 pokemon to my PC (10 Anniversary Celebi and Wishmaker Jirachi.) But when I open the game in mGBA, it says my file was corrupted and loads the previous save file which is... not exact? Like my save position is in the same area but off by a few steps away, and my party that originally had 5 pokemon in it was moved to the PC and exchanged with the last 6 pokemon in the box, making it look like they switched places. The pokemon I added in PKHeX don't show up at all in the PC, but still show up in PKHeX just fine. But if I save the game in mGBA and attempt to open it in PKHeX again I get the following error:

Attempted to load an unsupported file type/size.
File Size: 131088 bytes (0x20010)

I've noticed that untouched or edited in PKHeX first, my Sapphire files appear as:
Sapphire.gba (16,384 kb)
Sapphire.sav (128 kb)

But if I save in mGBA, they look like this:
Sapphire.gba (16,384 kb)
Sapphire.sav (129 kb)

mGBA makes the .sav 129kb instead of 128kb for some reason? Which confuses PKHeX? But not saving in the emulator is fine, but corrupts the player position/what's in the party and PC gets swapped if I edit the save in PKHeX? I've never seen this before. I'm not sure if this has to do with the RTC, as my copy of the game has a dry battery and mGBA seems to fix it because I don't see the dry battery message when I boot up. There's no issues with the pokemon in PKHeX either, they're just event pokemon and pass legality.

Is there a way to fix this or am I doing something wrong? I just wanted to backup my save file and add event pokemon with PKHeX and save it to my physical game with the Joey Jr afterwards.

EDIT: I tried using a different emulator, Visual Boy Advance, and it still corrupts/bugs out after editing the save in the exact same way with PKHeX, despite the .sav file being the same 128kb.

Pokemon - Sapphire Version (USA, Europe).SAV

Edited October 27 by WitchDianna
additional info provided

[whoisme]

mGBA usually adds 1kb to the save file. This is resolved by opening the .sav file with a hex editor and deleting the last line.

[WitchDianna]

14 hours ago, whoisme said:

mGBA usually adds 1kb to the save file. This is resolved by opening the .sav file with a hex editor and deleting the last line.

So there's no way to disable this in mGBA? And why is the save still getting corrupted after switching to another emulator that keeps the save file at 128kb and doesn't add an extra line?

[WitchDianna]

I suppose you can't ever use a dumped file that has as dry battery or else it will corrupt the save file on an emulator and physical cartridge, unless you replace the battery. Very disappointing PKHeX doesn't work right for that sort of thing, I guess I can't use that game and just have to use something with a fresh battery or no battery and hope no corruption happens to the physical cart from editing. I don't know hex editing or coding, so I have no way to edit the file to prevent it from adding an extra 1kb.