Seems easier to me to append the ',' + value on the end of the hash values as you first read them in...

my %hash;
while(<>) {
    chop;
    my ( $k, $v ) = split /\s*\=\s*/;
    $hash{ $k } = defined ( $hash{ $k } )
        ? $hash{$k } . ",$v"
        : $v;
}
while ( my ($k, $v ) = each %hash ) {
    print "$k = $v\n";
}
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