Pool Builder here.
Man what a nightmare. I hope you figured out a solution but thought I would chime in just Incase. The simplest solution on this would be to raise the bond beam all around and shoot in an extra 2 ft on top of everything in the shallow end and spa. Whether this works with the grade that surrounds your pool I don’t know. If it does just make sure you have adequate drainage between your house and pool. You typically don’t want your pool higher than the foundation on your house to mitigate foundation issues.
Another idea is to leave the whole bond beam extending 2ft out of the ground and to finish the outside with stone, tile or stucco (like your Spa but the whole pool) Keep in mind though that a raised bond beam does typically call for extra steel since it has no soil around it to add strength to the wall.
If none of these solutions work for your application and Demo is required I would demand all further work to correct the issue be inspected by your county inspector. Including Steel plans, epoxy application and soil conditions. If they demo the bottom of your pool and dig it deeper and end up in a different color or textured soil that can lead to serious structural issues so absolutely demand a soils inspection.