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You can replace the Multi-Melta with a TL Autocannon. That's all well and good.
You can replace the Dreadnought Close Combat Weapon with a TL Autocannon. Again, that's all well and good.

But the built-in Storm Bolter on the arm with the Dreadnought Close Combat Weapon, is it lost or kept if you trade-in the DCCW for the TL Autocannon?

If the DCCW goes away, so does the built in weapon.

It is lost, same way you would lose it if the DCCW was destroyed,