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I solved transfering Pokémons with this problem to HOME and then retransfering back to Sword. Everything was fixed. Thanks @SkyLink24. (Then I used PKHeX to clear all HOME Tracker values).

be sure to use the legality mod version compatible with the PKHeX version you are using. I suggest you to use the latest build both for PKHeX and Auto Legality Mod. Also, be sure to put the mod dlls in the "plugins" folder in your PKHeX directory and check that the DLL are not blocked (Right click on DLL -> Properties -> check if there is a checkbox called "Blocked" and if so, uncheck it).

v1.2 - August 12, 2020 - Fixed header information - Restored DSi related information Patch Downloads: https://projectpokemon.org/home/forums/topic/24126-pokémon-blaze-black-2-pokémon-volt-white-2/?do=findComment&comment=274862

I don't think there is one. Note: what I'm about to say only applies to bootleg copies that stores the save as a sector of the rom dump. Not every bootleg treats saves this way. For starters, learn how to find a save in your rom dump using hex editor. Once you get that done, learn how to replace the save in your rom dump using hex editor. If you cannot get the above 2 points done, no point worrying about restoring the save.

Reload the page, and read what I said. I've made that edit quite a while ago. Based on what you're quoting, you've missed what I edited in.

@KMSteter_88 it basically means you (and other parties you mentioned) didn't attach a proper save file. Nothing wrong with PKHeX. You mentioned you're using a repro cartridge? For your case, the save is stored in the ROM (cause it's a bootleg isn't it. That's how some store saves). Dump the ROM and run it through this program. Reminder: do not upload the ROM here.

When you transferred the save to VBA it took saved the time your computer was set to as the newest time you played the game in the save game. Then you transferred the save back to the original cartridge that had the RTC still showing a older date, effectively time travelling into the past. The game is just waiting until the RTC catches up and passes the date and time you played it on the computer. You can easily fix this by running the homebrew RTC changer to set the cartridge to the current real date. Then after that you can transfer the save back and forth all you want with no problems. Here is the homebrew, two versions one a GBA multiboot file and one a NDS homebrew for use with a NDS flashcart in a 2 slot system https://github.com/megaboyexe/GBA_RTCRead

VBA has been known to screw with the RTC function. There should be an option to disable the RTC in VBA which might help.