The actual reason you aren't substituting properly is that you are printing @L1, but that array never gets modified by your substitution which acts on $line.

Not true:

my @L1 = qw(Abc aBc abC);
for my $line (@L1) {
    $line =~ s/a/_/i;
    print "\@L1: <", join(", ", @L1), ">; \$line: <$line>\n";
}

__END__
@L1: <_bc, aBc, abC>; $line: <_bc>
@L1: <_bc, _Bc, abC>; $line: <_Bc>
@L1: <_bc, _Bc, _bC>; $line: <_bC>
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