Open the input file once and use a single while loop.
Pass the number to the querysub as a parameter and return the result.

#!/usr/bin/perl
use strict;
open my $fh_in,'<','input.txt' 
     or die "Could not open input $!";
open my $fh_out,'>','output.txt' 
     or die "Could not open output $!";

while (my $var = <$fh_in>){
  if ( $var =~ /(.*Entry\s*)(\d*)(.*)/ ){
    my $qresult = querysub($2);
    print $fh_out $1.$2.$qresult.$3."\n"; 
  }
}

close $fh_in;
close $fh_out;

sub querysub {
  my ($num) = @_;
  return "[Result with $num]"; # test
}

#input.txt
#  Entry 1 abc
#  Entry 2 def
#  entry 3 hij
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