c:\@Work\Perl\monks>perl -wMstrict -e
"my @lines = (
   qq{.024. 3# keep this one  \n},
   qq{.024. 3#  \n},
   qq{.024. 3# keep this two  \n},
   qq{.024. 3#|a9780750247092|xisbn13\n},
   qq{.024. 3# keep this three  \n},
   qq{.024. 3#|a0750247096|xisbn\n},
   qq{.024. 3# keep this four  \n},
   );
 print for @lines;
 print qq{\n};
 ;;
 my $rx_first = qr{ [.] 024 [.] }xms;
 my $replace  = '.020.';
 ;;
 LINE:
 for my $line (@lines) {
   next LINE if $line =~ m{ \A $rx_first \s+ 3[#] [ ]{2} \Z }xms;
   $line =~ s{ \A $rx_first (?= .* [|]xisbn (?: 13)? \Z) }
             {$replace}xms;
   print $line;
   }
"
.024. 3# keep this one
.024. 3#
.024. 3# keep this two
.024. 3#|a9780750247092|xisbn13
.024. 3# keep this three
.024. 3#|a0750247096|xisbn
.024. 3# keep this four

.024. 3# keep this one
.024. 3# keep this two
.020. 3#|a9780750247092|xisbn13
.024. 3# keep this three
.020. 3#|a0750247096|xisbn
.024. 3# keep this four