Catch them all challenge

Im going to do this, already sorted my box into order for the kanto and johto part of the dex. Im doing this on Soulsilver and have emerald, diamond, platium and heart gold.
 
I might want to sign up for this challenge but I don't want to transfer all of my pokemon to one game. For example, I have a number of pokemon all on my Fire Red version and transferring six a day to my Platinum version would be torture. I also have Mew on my Yellow cartridge. Would it be okay to record all progress but from different game versions?
 
I guess i will do this on Soulsilver

367/493 :D

yes i will update later...
 
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