3DS files are easy to confuse with DS files because the names sit next to each other in search. A DS game is one .nds. A 3DS game might be a .3ds, a .cci, or an installable .cia, and the interesting mods are often a LayeredFS directory of replacement files rather than a binary diff of the whole card. If the download is a folder with a readme that says to drop it on an SD card, a ROM patcher is the wrong tool. I say that at the top so the rest of the page is for the cases that really are a patch.
When a project does ship an xdelta, the size jumps again. A complete 3DS image can require substantially more memory than its patch file. The same memory warning as the DS page applies, only more so. Desktop xdelta3 is the default recommendation once the image no longer fits comfortably in a tab. The browser still applies smaller diffs. Secondary compression messages are unchanged from other xdelta files. They are not a 3DS-specific cipher.
Encryption and trimming matter more here than on GBA. A patch hashed against a decrypted image will not match an encrypted dump, and I will not invent a universal decrypt step. Follow the author's input description. If they do not publish a hash, the only verification I can offer is the patch's own checksum, if the format has one. xdelta's check is optional. A silent apply is weaker evidence than a BPS source CRC.
I am not linking CIA download sites. This page explains the fork in the road: LayeredFS folder, or a real diff, or a file you should not expect this tool to rewrite. The DS guide is the neighboring cartridge page. The xdelta guide covers the diff format itself.
