How does PKHex handle transfers from one gen to the next and back?

[BenFerd]

Okay so, I know it's a weird question, but I would like some input regarding this. 

A few years back I extracted my Emerald save and continued it on an emulator. Then, I got a couple 'mons I wanted to keep, threw them in PKHex, gave them to a bot and traded them to my SwSh. 

I have since gained the ability to do the transfer legit, however I lost that save (only the continuation/what I did in the emulator, not the whole thing) and the Pokémon files

Options are 

A) Do whatever I did again (please no; it was the entire Battle Frontier from breeding to completing all Golds) 

B) Trade the 'mons back to the bot, get the files, pass them through PKHex back to Emerald and then do the transfer legit

My question is, if I input the files in the same Emerald save (or some hours back, whatever) , do they "revert " back to how they were before PKHex made the changes to make them appear transfered, or are they created anew? Essentially, do they "*remember " they are from that Emerald save due to the OT info, or does that not matter and they are completely new Pokémon? 

 

Thanks a lot in advance!