I suggest that you hire an attorney to look after your interests. For example, did the live-in have a signed Power-of-Attorney (POA)? Did the live-in report your father's death (i.e., was she going to continue to collect his SS checks by not reporting his death?)? Who has property rights to his home? Can you have a court declare that you are the executor of his estate? There are many questions here that go far beyond the tax issue.
Just marking him as deceased on his return will not solve most of your issues; I suggest consult an attorney instead.
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