Is the issue here that you're trying to buy the house from the bankrupt estate and hope that the trustee's estimate is low, or that you're trying to establish as much equity as possible and are hoping for a high estimate? Submitting appraisals to a court to help establish the value of real estate is quite routine.
I don't know anything about when or how the house was purchased or the length of the marriage, so I'm not positioned to guess whether the judge is being reasonable in holding that the home has merged into the marital estate despite your greater initial contribution.
You have a divorce pending, so you should be able to discuss these issues with your divorce lawyer.

