The .cia archive is just a patch, ou it´s a rom for the citra?
A .cia is a packaging format that holds NCCH files. NCCH files are basically like ‘’.exe’’ files. They can hold game data, update data, dlc data, ect. .cia files are installed directly into a 3ds’ or Citra’s nand or sdmc folders, which makes the installed files unable to be moved around on your PC after they’ve been installed. If you want to remove them after having installed them for some reason (maybe a bad dump?), you’d have to do some manually. Hence why it’s not recommended to dump actual games in this format even if it’s possible. It’s better to dump Installed Titles as .cxi files instead as they function identically to .3ds files in Citra. Only update files and DLC should be dumped in the .cia format for use in Citra.
.3ds is also a format that holds NCCH files, though instead of installing those files to your sdmc folder, the .3ds file can simply run itself in Citra directly without issues. Meaning you can move the .3ds around as you please and store it where you want. (important for those that want to save space on their C: drive.)