This should work in theory, but it will clash with a basic restriction of the Files folder, no duplicate file names.
Importing the files of the first export will be fine, after that if you try to import a new file that has the same name as an existing one, the old file will be updated.
Even if a new unique name was assigned to each file so everything was imported as expected, the name changes would probably break the exports.
A possible solution I am thinking about would be compressing each export in it's own zip file, then importing each zip file with a unique name. Doing that you should be able to keep each export intact because C3 doesn't actually get to see the compressed files.
Then you would need some scripting to decompress a zip at runtime and show the contents in the iframe. Assuming you also import zip.js to handle decompressing the zip files at runtime, it shouldn't be too difficult... depending of course on how comfortable you feel about scripting. What I just described will be pretty difficult if you are not comfortable scripting.