I got my second 3DS last year, one is up-to-date, the other one is for PKHeX (not updated) and I had no problems hacking Mons. I would mainly use 2 methods to inject: One of them was with QR Code method and the other method was the PC OUT-PC IN method where I could edit my whole box from the My PC very easily.
I have not hacked anything in the game for 3 months but now that I try, I am having a problem. Using the first method, QR Codes, it is okay (nice, quick and effective way :] ), but when I try the second method, PC OUT-IN, it will not work anymore and I am a bit confused. When I used to save the game and tried to PC OUT, the page would go green and then crash, after I would extract the SD Card and everything okay (if there was any problems I would just delete Cookies and History), but now the page will not crash, just says "no connection", so the method does not work anymore. I honestly do not know what is the problem, I have not updated the PKHeX console, it is still the 9.5.0-22, the last version before the PKHeX patch. I have checked if the files in the SD Card are okay and made sure that the Bookmarks of PCOUT-IN have the right URLs. I honestly do not know what is the problem and I was thinking you might know the cause of this. It is not terrible I suppose, I can still use the quick QR Code method, but modifying your box on the computer was very useful :[.
Another quick question is if it is worth it for me to upgrade to Homebrew? If so, do you know if they have patched the capability of installing it in the latest updates?