Probably one of your workers has a wrk_surname of O'Reilly or some such. You should let DBI do the quoting, replace your UPDATE loop with something like

my $upd = $dbh->prepare("UPDATE new_entrant SET forename=?,surname=? W
+HERE emp_no=?") or die $DBI::errstr;
while (my $row = $sth->fetch) {
    $upd->execute($wrk_forename, $wrk_surname, $wrk_emp_no) or die $DB
+I::errstr;
}
$upd->finish();
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BTW is your sep_char really "\\~" i.e. '\~' (the two characters "backslash" and "tilde"?