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";
  }
}