I hate to fall back on our standard reply that you need to go see an attorney about this, but you need to go see an attorney about this. Unfortunately, the attorney you used to file the case in the first place (assuming you had one) may now feel that he/she is not able to assist you due to the conflict between your interests due to your separation. There are far too many variables that will affect your situation and how much you may have to pay for me to give you a simple answer. You really need to speak with a local attorney who can review the case and advise. This may not be something that an attorney will do in a free consultation.
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When you two filed jointly, your attorney told you about the potential future conflict. Now that conflict has come to fruition and at least one (or possibly both) of you have to find a new attorney.
The above is general legal and business analysis. It is not "legal advise" but analysis, and different lawyers may analyse this matter differently, especially if there are additional facts not reflected in the question. I am not your attorney until retained by a written retainer agreement signed by both of us. I am only licensed in California. See also avvo.com terms and conditions item 9, incorporated as if it was reprinted here. Please visit my web site: www.avanesianlaw.com for more information about my services.
The joint debts will be unaffected by a bifurcation of your case. You each would have to list all your debts anyway, including joint ones. As for your payment amount, you would likely be looking at a modification of your confirmed plan due to your changes circumstances. These are really good questions, and ye person best equipped to answer them for you is your current chapter 13 attorney. Your attorney will have the information needed to answer more accurately and completely.