First of all I want to thank everyone for helping with the first error I was having. I was able to get the code cycling through the files, however now I'm running into an error doing a regex substitutions.

#Find the CHAN pair
            if( $UNID[1] eq $UNID[$x] )
            {
                #Temporary variable to store the CHAN
                $channel2 = $CHAN[$x];
                
                #Creates a loop counter
                $y = 1;
                #Tracks if the changes have been complete
                $complete = 0;
                
                #Search the files for the instancs of the CHAN
                while( ( $y < scalar( @FILES ) ) && ( $complete == 0 )
+ )
                {
                    #Open the file for replacement
                    open $fd, '<', $FILES[ $y ];
                    #Creates a backup of the original file
                    $^I = '.bac';
                    
                    @file = <$fd>;
                    
                    seek $fd, 0, 0;
                    
                    print "$channel1 and $channel2\n";
                    
                    foreach $file ( @file )
                    {
                        $file =~ s/$channel2/$channel1/ or die $!;
                    }
                    
                    #Close the file that was searched
                    close $fd;
                    
                    $y++;
                }#End replacing while
                
                #Remove the used entries from the array
                delete $CHAN[1];
                delete $UNID[1];
                delete $CHAN[$x];
                delete $UNID[$x];
    
                #Force the loop to end
                $found = 1;
            }#End pair find if
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For some reason the line containing the studstitution errors out saying the variables are uninitialized. But I can put a print statement directly before them and that will print the values just fine. If I a use an or die statement I recieve an error just saying that the program died. Any help would be greatly appreciated. Thank you.