You only print lines to your output file when they contain no whitespace.

if( /^(\S+)$/)
   {print OFILE"$1\n\n"}
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From your input that may not be what you want. Are you after the first contiguous sequence on each line AFTER the first text with the scaffold<num> or just the entire line with the first part altered?

It would also be good practice to explicitly close your files when you are finished reading/writing them.

Update

    # this may help
    while (my $line = <FILE>) {

       # The entire line with a substitution
       # if( $line =~ s/^>\S+\/>contig_$count) { 
 
       # Substitution and 1st contiguous sequence         
       if( $line =~ s/^>\S+\s+(\S+)/>contig_$count $1\n/) {
       print OFILE $line;
           $count++;
       }
   }
   close FILE;
   close OFILE;
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Cheers,
R.