PkHex Problem - Gen 1 Box Slots

[Deadshot626]

When trying to load my Pokemon Yellow or Blue save via JoeyJoeBags to an authentic GBC Cart, it shows that there are only Pokemon in Box 1 even though I have multiple Boxes filled with Pokemon through Box 8 when importing them through Pkhex. All the items added and everything show up correctly, but just Box 2 and on don't appear. If I save on Box 2 before exiting PkHex, then load the save back onto the cart, it will show that all of Box 2 is full in game but the rest empty, even Box 1. So depending on the Slot that I save Pkhex on, is the slot that will appear with all the Pokemon in game, but the rest will be completely empty.

This issue was occuring on Pokemon Red until I tried making new save files a couple times and somehow now all 151 Pokemon show up in the boxes but just can't seem to get the same thing working for Yellow or Blue. The problem isn't making any sense to me so I was hoping someone would know a solution or had similar issues before.
 

Thanks in advance!

[Deadshot626]

I figured out the solution to these problems. All you need to do is dump the edited save back from your cartridge onto your pc, it will show that Slot 2 and so on are empty when loading the save in Pkhex. Now just load the Pokemon back onto the save and restore that save file onto your game and it should now have all Pokemon in the PC Boxes that originally should have been there. Not sure why it doesn't work the first time but this seems to be the only fix I could find.

But I have another issue. When changing the Trainer Name on Pokemon Yellow, Pikachu will stop following the trainer, even if I alter the OT of Pikachu to match the new Trainer name and the IDs even match. Does anybody know how to get Pikachu to follow you again or a fix for this?

Edited April 18, 2019 by Deadshot626

[theSLAYER]

1 hour ago, Deadshot626 said:

But I have another issue. When changing the Trainer Name on Pokemon Yellow, Pikachu will stop following the trainer, even if I alter the OT of Pikachu to match the new Trainer name and the IDs even match. Does anybody know how to get Pikachu to follow you again or a fix for this? 

Pretty sure as long as OT and TID both matches exactly, there isn't a problem.
Deposit the chu then withdraw it, see if it works.

[wuxbustah8]

The original issue still seems to be a problem.

I've tried the "solution" given above many times, but still can only seem to have the Pokemon in Box 1 show up.

[wuxbustah8]

I took a video to show the error I'm having.

 

[Atrius97]

Kurt/Kaphotics figured this issue out in the PKHeX Dev server.

Quote

Probably some unrelated flag that stores if a box has pokemon data, that was never set by your "really early game progress" save file
actually lol, looks like it is the game cleaning itself to remove junk data for fresh saves accessing the box for the first time.

You need to progress the game further/open your boxes at least once before trying to edit the game in PKHeX. This isn't a bug with PKHeX, it's a feature of Pokemon Yellow.

[wuxbustah8]

Thanks. 

For future reference to anyone seeing this, all that needs to be done is change the box once, save, and then edit that save.