EV Training in Emerald

[Eclipse628]

To start things off I want to say the only reason I got my epilogue device was to use pkhex to fix the RTC for Emerald. I just got into EV training on my old Emerald game and someone said that for level 100 pokemon all you need to do is put them into the PC and the stats will update, I've come to find out that is not the case. I already went through all the battles to EV train to find out I wasted several hours. I would like to know if I can edit the EVs and if my Pokemon will remain legal after I do so

Thank you all in advance