It sounds like the partners' mortgage payments for their residences are being paid by the LLC. If these mortgage payments are not business expenses, then Yes, these would be distributions to the members and would reduce equity. They are not different that cash payments to the owners. These payments should be charged to, or reclassed as Owner Distributions.
There are additional reporting requirements for partnerships (LLCs filing Form 1065) that have negative capital accounts. For more information, see:
Negative Tax Basis Capital Account Reporting Requirements
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