Hello to the monastery!

First, in the for loop of the second block I think you should use $var2 instead of $var in the if condition. The Perl compiler told me this after I inserted

use strict;
use warnings;
[download]

at the beginning, which is recommended.

Second, the g modifier in the second block

    if ($rows[2] =~ m/\[R\]/g) {
[download]

skips the first [R] of the second column. So, it is not available any more for the next match.

If I change your script to

use strict;
use warnings;

open (OUTFILE, "< History21.txt") or die "Could not open source file. 
+$!";
open (NEW_MED, "> History_MED1.txt") or die "Could not open med file. 
+$!";
open (NEW_SUR, "> History_SUR1.txt") or die "Could not open sur file. 
+$!";
  
my $count2 = 1;
while (my $line = <OUTFILE>) {
    my @rows = split(/\|\|/, $line);
    if ($rows[1] =~ m/\[R\]/g) {
         if ((my @var)= $rows[1] =~ m/\](.*?)\[/g) {
             foreach my $var (@var) {
                 if ($var =~ /^\s$/g) {
                     #DO NOTHING SINCE WE ONLY WANT IF THERE IS ANYTHI
+NG INSIDE THE 2 R BRACKETS
                 }             
                 else {
                     print NEW_MED "$rows[0] || $var\n";
                 }
             }
             
         }
      }
    if ($rows[2] =~ m/\[R\]/) {
         if ((my @var2)= $rows[2] =~ m/\](.*?)\[/g) { # I AM ASSUMING 
+IT WILL RETURN SIMILAR TO THE PREVIOUS IF STATEMENT FOR ROW1 ABOVE
             foreach my $var2 (@var2) {
                 if ($var2 =~ /^\s$/g) {
                     #DO NOTHING SINCE WE ONLY WANT IF THERE IS ANYTHI
+NG INSIDE THE 2 R BRACKETS
                 }             
                 else {
                     print NEW_SUR "$rows[0] || $var2\n";
                 }
             }
         }
      }
      $count2++;      
}
  
close(NEW_MED);
close(NEW_SUR);
[download]

I get the missing output.

ZZZZZ00DFL  || No pertinent past medical history  
ZZZZZ00DFL  || No pertinent past medical history  
ZZZZZ00C4H  || High Blood Pressure  
ZZZZZ00C4H  || Kidney stones  
ZZZZZ00C4H  || SOAPP-R Score : Moderate/High Risk:  19  
ZZZZZ00C4H  || Sleep Apnea Assessment(STOP-BANG): ( 2/4 );  7/2/2014  
ZZZZZ00C4H  || Orthotic brace tried for pain relief: Yes: limited bene
+fit  
ZZZZZ00C4H  || TENS Unit tried for pain relief: Yes: limited benefit  
ZZZZZ00C4H  || Tried Topical Compound Cream?: Yes: limited benefit  
ZZZZZ00C4H  || Acupuncture therapy tried for pain relief: Yes: limited
+ benefit  
ZZZZZ00C4H  || Chiropractic therapy tried for pain relief: Yes: limite
+d benefit  
ZZZZZ00C4H  || Physical therapy tried for pain relief: Yes: limited be
+nefit  
ZZZZZ00C4H  || Massage therapy tried for pain relief: Yes: limited ben
+efit  \
ZZZZZ00C4H  ||  \
[download]

and

ZZZZZ00DFL  || UNREMARKABLE  
ZZZZZ00DFL  || UNREMARKABLE  
ZZZZZ00C4H  || Hysterectomy  
ZZZZZ00C4H  || Spinal Fusion: L4-5, L5-S!; 2010  \
ZZZZZ00C4H  ||  \
[download]

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