It looks like you're basically trying to compare two sets; one the set of sites split from $sites, and the other the set of new site numbers fetched from the database. I think the simplest way to compare sets is to use a hash or two. This example checks whether a new site number is in the set of sites:

my @sites = split ' ', $sites;
my %sites;
for (@sites) {       # there are shorter ways to do this step
  $sites{$_} = 1;    # but I'm going for clarity in this example
}

while ($sth4->fetchrow()) {
  if (exists $sites{$newSiteNumber}) {
    print "modify $newSiteNumber\n";
  } else {
    print "delete $newSiteNumber\n";
  }
}
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I hope I'm understanding your question, and that this code sample is helpful.

BTW, what is the undef in the call to bind_columns() for?