Oh well if it is writing over code... just get the value @ 02045808 and write it back with another activator code.
94000130 FCFF0000 (R+L)
52045804 E2431001
02045808 OLDVALUE
D2000000 00000000
Load your save file, dump to PKHeX's database.
Load this save file, dump to PKHeX's database.
Load your save file, import PKHeX's database.
No need to have multiple posted save files.
sky3ds cannot run edited roms or have edited save files as it is a fake cart; no code can be run.
signature checks need to be patched out, which sky3ds can't.
They're likely tied to event flags as they are event only; dunno.
I can't implement new features unless I know how they need to be implemented (I do not own a 3DS or the games...)
[TABLE]
[TR]
[TD]0030[/TD]
[TD]26200[/TD]
[TD]00000C48[/TD]
[TD]75F9A[/TD]
[TD]Pokemon Bank Gifts
0x25E44 - u16 checksum (ccitt16, 0xFFFF initial) of 0x25400-0x25E43[/TD]
[/TR]
[TR]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]0032[/TD]
[TD]27200[/TD]
[TD]00000200[/TD]
[TD]75FAA[/TD]
[TD]PGL Promotion Gifts[/TD]
[/TR]
[/TABLE]
PKHeX is pretty bloated as it is; this information is already on our wiki so anyone else can come up with a separate solution.
It was theoretically possible even back in B/W, but nobody ever took the time (2).
Not going to happen unless someone else is motivated to figure it out and reports back a how-to.
The two files you uploaded are identical; this is not an issue with PKHeX but either with SDF or Gateway.
Are you using a .cia? "Gateway" is too generic. ".cia" installed games have issues using SaveDataFiler.
BW/B2W2 only checked if you had the item, and did not check event flags or Pokedex status.
It's reasonable to assume that X/Y/OR/AS handle it the same way.