push(@arrCompletedChains, $strChain);
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As it says in perlsyn:

    If any part of LIST is an array, "foreach" will get very
    confused if you add or remove elements within the loop
    body, for example with "splice".   So don't do that.
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UNTESTED, but you could see if this is faster:

use List::Util 'first';

# sort largest first
my @sorted = sort { length $b <=> length $a } @arrWorkingCompletedChai
+ns;
my %to_delete;
# remove shortest first
while ( my $next = pop @sorted ) {
    if ( first { index( $_, $next ) >= 0 } @sorted ) {
        ++$to_delete{ $next };
        }
    |

@arrWorkingCompletedChains = grep !$to_delete{ $_ }, @arrWorkingComple
+tedChains;
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