What a misery. You should get some detailed advise from a business/tax lawyer or CPA with prior experience or employment with the IRS. You should not rely on any figures previously prepared by the TMP. The Manager(s) of the LLC(s) can appoint a new TMP. You should almost certainly go on extension for your filings. San Diego attorney Hillary Johns, who regularly posts on Avvo, may be a good first contact for you locally.
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.
The partnership can revoke the designation of the current Tax Matters Partner and can designate a new Tax Matters Partner, even for tax years for which a return has already been filed. The steps for making these changes are set out in the pertinent portions of the Treasury Regulations, 301.6231(a)(7)-1. The direct link to the electronic copy of that section is here: http://ecfr.gpoaccess.gov/cgi/t/text/text-idx?c=ecfr&sid=feea7efdf175c4d8918c475395cc9417&rgn=div8&view=text&node=26:126.96.36.199.188.8.131.52&idno=26
The bottom line is that you and the partnership(s) don't have to be left swinging in the wind because the current Tax Matters Partner is no longer competent to handle the tax matters. Given the seriousness of the issues involved the partnership(s) should immediately retain a tax attorney with experience in partnership matters and partnership audits to assist you and the partnership(s) in fixing up the mess the current TMP has left. Your tax attorney should also retain an accounting firm to help with preparing the unfiled returns and reviewing the prior years' filed returns to see if there is anything in the returns that needs to be amended. It is important that your tax attorney retain the accountants and be the filter for the material that is provided to the accountants so that the IRS is limited in its ability to force disclosure of the reasoning and decision-making behind any positions that are taken on any of the returns that need to be amended or, in the case of the unfiled returns, filed.
Please do this as soon as possible - like yesterday - and please do not say anything to any IRS agent who wants to speak with you, especially anyone who says they are a "special agent" - special agents are the IRS' criminal investigators and when they want to talk to you it's because they want to prosecute you - and make sure that all of your partners understand this as well. If anyone from the IRS does contact any of you, just politely refer that person to your attorney.
My answer does not constitute legal advice and may not be relied upon by anyone for any purpose and does not constitute an attorney/client relationship or an offer to form such a relationship. This disclaimer is intended to be fully compliant with the requirements of Treasury Department Circular 230 and the terms thereof are fully incorporated by reference. If you wish to consult with me please contact me at dwatchley@newyorktaxcounsel or visit my website at www.newyorktaxcounsel.com