Reading a file in slurp mode sometimes (always?) returns an empty string at end of file, instead of the more expected undef. I believe there are perlbug reports open on this.

Your problem is that you have read all the data in the file, so there is nothing left to read. Either rewind the file (seek FILE, 0, 0, or read it into $string originally instead of into @file. There is no problem with saying print FILE_BU $string; and then modifying $string and writing it back out to FILE (after rewinding it yet again, or you will just be appending to the original data.)