Then I was almost right.
No, you were completely wrong. :p
Perhaps an example will help. Our Exemplarian army has three commands each of 20 ME of fighting troops. Each command also has two elements of Irr Bge pooled as an army baggage command.
Each fighting command thus has a total ME of 20+2=22.
The baggage command has 6 ME.
The total army ME is 22+22+22+6=72 (this is where the "double counting" comes in: each baggage element counts 1 ME twice, once for its parent command, once for the baggage command).
If now some evil Didactian horsemen destroy one of the baggage elements, the baggage command now has 5 ME left (and the army 71). The fighting commands still have 22 ME each - they're "unaware" that the baggage's been sacked.
Is that clearer?