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Unfortunately, as they are still married medicaid could still seek to take the marital property, but this is only a presumption that the property is marital property and this presumption can be disputed in an appeal. To dispute the fact it is marital property, your mother will have to prove to medicaid that they have been separated from bed and board for 30 years and as such the property is not going to be considered marital. At this point, your mom needs to consider protecting herself by getting a divorce finally and having the court declare the property separate so that she does not have to fight with medicaid in the event of your father's death.
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