Answer: Your husband has a point, but before siding with him I'd have to do a little investigation. If the surface roots have, indeed, grown up into the soil in the raised boxes, removing that soil will expose the roots. I'd be inclined to dig down into the raised boxes to see whether or not tree roots are there. If you absolutely, positively need to remove the raised boxes, even though roots are there, I'd do it gradually, allowing the soil to settle around the roots and eventually weather away. This gradual process will allow the roots to either form bark (if they're going to be above the soil surface), or work their way back down into the soil where they will be protected. If you remove the sides of the boxes, the soil will escape as the area is exposed to rain (or water from the hose). If it erodes over a period of months, I think it would be better for the trees. You would end up with a mound of soil around each tree, which would eventually weather away.
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