G'day shoura,

Here's some techniques for removing redundant and duplicated processing.

• There's a single pass through the SEQ file. Trimming leading and trailing whitespace, as well as the line terminator, uses a single regex capture. The replacement text, for later use, is calculated once here.
• The regex for use when processing the TXT file is created once only.
• There's a single pass through the TXT file; and there's no nesting. The substitution, using values already calculated, is the only processing done here.
• I've used Inline::Files as the actual opening and closing of your files doesn't appear to need optimising. Having said that, I would urge you to use lexical filehandles throughout, and the 3-argument form of open.

#!/usr/bin/env perl

use strict;
use warnings;

use Inline::Files;

my %seq;

while (<SEQ>) {
    my ($trim) = /^\s*(.*?)\s*$/;
    ($seq{$trim} = $trim) =~ s/\h+/bbb/g;
}   

my $re = qr{(@{[join '|', sort { length $b <=> length $a } keys %seq]}
+)};

while (<TXT>) {
    s/$re/$seq{$1}/g;
    print;
}   

__SEQ__
          scooped up by
          social travesty
          without proper sanitation
__TXT__
Many of them are scooped up by chambermaids, thrown into bin bags and 
+sent off to landfill sites, which is a disaster for the environment a
+nd a social travesty given that many people around the world are goin
+g without proper sanitation.
[download]

Output:

Many of them are scoopedbbbupbbbby chambermaids, thrown into bin bags 
+and sent off to landfill sites, which is a disaster for the environme
+nt and a socialbbbtravesty given that many people around the world ar
+e going withoutbbbproperbbbsanitation.
[download]

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