As a temporary fix I would suggest that adding half the Shield value to Armour and then zero'ing the Shield values is the way to go, rather than adding the whole amount.
That way, you get additional toughness at the front which works for missiles as well as melee, it does not mess up the autoresolve to the same extent that a large defense value would (and the autoresolve correctly matches what happens in battles), and the fact that toughness in the frontal segment is not as high as it should have been given the original stat-balance will be compensated by fewer casualties from rear and flank attacks over the course of the battle.
Increasing armour by too much while removing shields will decrease the influence of the positional play aspects of the game, and devalue fast-moving units, so you'd want to avoid that.
You could then also add a further half-shield-value to defense, which would bring frontal melee strength up to the intended value, but you'd probably want to test the half-shield add to armour by itself first to see exactly how much difference the added armour makes against rear and flank attacks in a variety of battles. Adding further defense just for melee attacks might not be justified.
Hopefully that helps some.
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