So, the file name (indeed, the inode) of the first file is now being used to store the new script? Sounds more like a server/file permission problem than a problem of script content.

Do either you or your friend remember what was done a year and a half ago when that first file was installed and made to run? Are you sure you repeated the same steps this time when trying to install a second file? Are you sure the folks who run the server haven't changed policy since then -- e.g. no more new cgi scripts without some additional check/approval/blahblah? (Who knows? Maybe they put in a check to see if a perl cgi script has "-T" on the shebang line.) If there was a policy change, it's possible that it applies only to new stuff, and existing script files were allowed to continue operating.