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So I was looking over the options that a command squad has and noticed that the company champion seems to be a bargain, for the cost of a power weapon you can upgrade one member to have a power weapon, combat shield, and WS 5. But I couldn't help but notice that it's very unclear on how his gear works, since he is an "upgrade to a Company Champion with a power weapon and combat shield" I get the feeling these are in addition to his old wargear since there's no clear reference to replacing items which there tends to be in the newer codices.

Would you guys agree or does he lose his boltgun/bolt pistol in the process of upgrading to the company champion?

Agreed, he retains all equipment.

I was struggling with the same predicament, but until told otherwise I'm gonna play it as RAI, and allow him to keep said weapons.

RAW he is upgraded, nothing is replaced. You get a hefty CC upgrade for a small fee.