ROM Hack The "Ask" section won't let me ask, so here I am; need PK3DS help

[IAmSoLost]

I dumped Pokemon Y from a 3DS and used ctrtool to extract the contents, creating 2 folders - exe and romfs. Those 2 folders are stored in another folder simply called Y. Whenever I open Y with pk3ds, a prompt appears saying "Detected Compressed code binary. Decompress? Files will be replaced." I don't know if this should happen or not, or how to fix it. Clicking "yes" or "no" takes me to the menu as normal. However, if I try to edit something in the ExeFS tab (the Shiny Rate, for example), it tells me ".code.bin not decompressed. Aborting." followed by "Unable to find PID Generation routine. Closing." Did something go wrong in the extraction process? Or is it some other issue? In either case, do you know what to do?

 

[IAmSoLost]

Nevermind, I figured it out.

 

[Praetor_]

I dumped Pokemon Y from a 3DS and used ctrtool to extract the contents, creating 2 folders - exe and romfs. Those 2 folders are stored in another folder simply called Y. Whenever I open Y with pk3ds, a prompt appears saying "Detected Compressed code binary. Decompress? Files will be replaced." I don't know if this should happen or not, or how to fix it. Clicking "yes" or "no" takes me to the menu as normal. However, if I try to edit something in the ExeFS tab (the Shiny Rate, for example), it tells me ".code.bin not decompressed. Aborting." followed by "Unable to find PID Generation routine. Closing." Did something go wrong in the extraction process? Or is it some other issue? In either case, do you know what to do?

What did you do I'm having this issue with no luck