IF the structure of the pool is sufficient, AND the dirt UNDER the pool is stable, THEN you can raise the bottom.
I've done it. There are several ways to do it. Regardless, trying to blend the new bottom into the old is a trick that may not succeed. Also, it won't be cheap, in part because it's non-standard work and your builder will have to use his 'smart' workers on YOUR pool, instead of scattering them around. You may have to wait till fall, just to get out of the busy season, so your builder can focus on your pool, without crippling other jobs he's working on.
Since you are this far along, there's little to lose by finishing it. I'd recommend going with what you've got, making sure it all works properly. Once it's full, you can see if it's as bad as you think, and make a decision.
Keep in mind that -- because this will be very NON-standard work -- your warranty may be compromised.
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