Dracofeu

So after more trials I ended up finding  the culprit, I  think.

It  seems that when I send my save data  over wifi using Filezilla, something happens in the process that ends up corrupting  the save. Why  this only happens to my Omega Ruby save and not the other Pokemon saves, I have no idea. So the solution is to plug the micro SD directly to the computer, that way no corruption happens and PKHeX is able to open the save again.

Thanks for your help @theSLAYER !

1 minute ago, theSLAYER said:

You device has CFW right?

Yes.

1 minute ago, theSLAYER said:

and your Omega Ruby is cart? are you certain your cart is real?

No, it's in the SD card.

1 minute ago, theSLAYER said:

If you restore the Treecko save into OR, does the game load?

Yes.

8 minutes ago, theSLAYER said:

Well the other saves are fine. If you think it's Checkpoint, try backing up using JKSM instead and see how that goes.

https://github.com/J-D-K/JKSM/releases
 

Just tried it, same issue

Oh sorry for the  confusion, the save in the OP (which doesn't work with  PKHex) is my actual Omega Ruby save (40+ hrs of gameplay,  8 badges) , thinking that there was a problem with the way Checkpoint backs up my saves I started a new OR save to test, which works just fine with PKHeX. Which leaves me questioning as to why my actual save won't work knowing  that the steps  to backup/retrieve the test OM save and my actual OM save are the same.

Hope I didn't make more confusing.

15 minutes ago, theSLAYER said:

as of now, I cannot be sure that you're exporting and importing the right save.

Maybe try exporting a different save, and uploading that different export to us.

I attached both my main Pokemon Y save and a Pokemon Omega Ruby test save after receiving the starter and both work with PKHeX. My main save of Pokemon OM attached in the OP has been retrieved in the same way but somehow does not work.

Thanks for your help btw !

Pokemon Omega Ruby Pokemon Y

4 hours ago, theSLAYER said:

Have you received a starter and saved in-game?

Also, when I loaded up your save in OR, there's this message.

Going back to your story, are you absolutely sure you're dumping and restoring the save correctly?
 

Yeah I'm about to tackle the  Elite 4 in the save that  I linked. It's really weird that it shows  that it's corrupted since I restored the backup to make sure that it's backed up properly  

And  I don't understand why my Y and UM (and even OM a couple days ago) work using the same method.

Hi,

Recently, whenever I transfer my save from my  3DS to my laptop and open it with PKHeX,  I get this error. At first, I thought it  was Checkpoint that was messing  with the save, but I tried the  same method with my POkemon Y  and UM saves and they both opened normally. Hell I even erased my OR save and started a new one and that one works but as soon as I restore my main  save, it stops working with  PKHeX.

Attached is the problematic save.

Thanks for  any help  !

main