I decided I wanted to play a randomized version of Pokemon X, but never used Citra before. So I followed a tutorial and it worked. The question I have though once I have the randomized game file, what do I do with the other files that were created alongside the randomized Pokemon X file, can I delete it or do I save it? For example, the Extracted Banner, ExtractedExeFS, DecryptedExeFS.bin, etc.
You may delete it, citra only cares about your .3ds/cia/cxi file.