if ( ( $flag1 or $flag2 )
 and ( length( $string ) )
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This is where lining up your delimiters makes a lot of sense. Had you lined up the interior parens, giving

if ( ( $flag1 or $flag2  )
 and ( length( $string ) )
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the unbalanced leading paren would be a bit more obvious; in fact,

if ( ( $flag1 or $flag2  ) and
     ( length( $string ) )
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might be even better: the if's leading paren isn't "masked" by the and.

In this case, though, I'd be sorely tempted to break the if's condition out into a small sub with a meaningful name. I think

if ( &condition( $flag1, $flag2, $string ) )
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is plenty readable, and gives you less punctuation to worry about.