Re: Sewer trench mound
What you describe is extremely common. I personally go to the extra effort to remove debris (roots/garbage ), but not stones. IMHO, it isn't all that hard to compact the soil a bit as the trench is backfilled, especially if backfilled with a backhoe or excavator. If filled with a bladed implement, then all you can do is drive over the mound to try to compact it a bit, but still leaving a bit of a mound when finished. Settling of the dirt will depend on how wet it is, and how much rain you get on it now that it's back in place.
I've done a number of trenches 12" wide and 36" deep, when the dirt is replaced, the mound has always been 6" to 10" in height. Most of the time this will settle to just about flush, though you should expect to need more fill in some areas or level others.
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