Welcome to PB!
I can see your concern. A full foot seems like a lot. I'm far away from being an expert on pond building (or even dirt for that matter), but have to ask...Do you think it was clay that settled or could it be a fair amount of top soil only?
If it was clay, that area did not get compacted properly, or at all. My old pond had its dam breeched so that it could be drained and renovated. No sheep's foot compaction when the 10 foot wide crevice was refilled at my pond; only bucket tamping the layers and the tracks as it laid the layers down. It did not settle any visible amount and it's been 4 years.
It's hard to say if you will have a problem. What does your contractor say about the settling?
