I believe .cci files are the same as .3ds files (two extensions same format). So, you can just rename one to the other.
I don't know about FBI, but l think Citra plays .cci files just like .3ds files. If FBI supports .3ds files, just rename the .cci files to .3ds and try them.
See the following link (this link is old. Citra supports .cia formats now):
https://community.citra-emu.org/t/3ds-vs-cci-rom-file-formats/191
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with "batch cia 3ds decryptor" if you try to decrypt a .cia GAME file , it seems to just extract the .cci/.3ds file from it and decrypt that.
If you try to decrypt a DLC/UPDATE .cia file, it seems to keep the format as .cia
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With "3ds + cia rom script" it seems to decrypt ANY .cia to a .cia file.
It has the ability to do conversation between .3ds and .cia from its conversation menu.
With using "3ds + cia rom script" I've never had problems with any decrypted .cia DLC/UPDATE files even though it always gives me the warning.
(only used them with Citra)