Now that's strange, did it happen on nutaku or dmm version? Also did you run any script before running the full art file?
The "info_eidolon" folder should only have about 60 (nutaku) or 84 (dmm) files, if you have many more than that then you should delete it and run again. If it is not the case, you should check the config.ini file and see if you recognize any N/R/SR eido name in there, file size should be about 241KB (nutaku) or 287KB (dmm), if you can spot any problems, just delete it and run "3_write_config" file again.
*Edit: I found the problem now. For some reason the folder in my zip file still have the old eidolon files and I was sure I had deleted them... :facepalm:
Anyway, you don't have to delete the whole folder, just delete the files from 2.json to 1026.json for both nutaku and dmm versions, that should fix the problem.