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I really doubt that it's the intent to disallow a magus to reduce the arcane pool bonus if their weapon is too heavily enchanted already. The precedent for being able to reduce spell caster level, and for high-level bards being able to activate bardic music as a move action if they want to perform a different swift action on their turn, both support the idea that you can "dumb down" a class ability if it's beneficial to you. I'd file that under the same category as Oracles using Spiritual Weapon in terms of strict RAW being clearly against intent.
EDIT: actually, I don't think it is RAW that a magus has to add all their bonus.
For every four levels beyond 1st, the weapon gains another +1 enhancement bonus, to a maximum of +5 at 17th level. These bonuses can be added to the weapon, stacking with existing weapon enhancement to a maximum of +5. Multiple uses of this ability do not stack with themselves.
"Can" implies not adding is an option. "These bonuses" implies each point of bonus can be assigned separately, with "do not add" as an option for each bonus.
That said, a magus will still have problem adding the Brilliant Energy property to a +7 or higher equivalent weapon without more significant favourable house rules.