I don't think substr is your problem:

#!/usr/bin/perl

my $pad = 100_000_000;
my $s = 'a' x $pad;
$s .= 'qq was here';
$s .= 'b' x $pad;

print substr( $s, $pad, 10 ), "\n"; # qq was here
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If you save the return from editcontig to a file, and find the character position that should be the start of the substr, is it actually off?

Its more likely that editconfig is stripping out more or less than it should. Perhaps there is some other character in your longer file? BTW, you can condense editconfig to something like:

sub editcontig {
  my $rawseq = shift;
  $rawseq =~ s/\s+//g;
  $rawseq =~ s/[0-9]//g;
  return $rawseq;
}
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and you could validate the output by adding:

if ( $goodseq =~ /([^actg]+)/ ) {
  die 'found unexpected character $1";
}
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qq (who knows nothing about genes)