The IRS instructions for Form 5695 specify that both you and your spouse owned and lived apart in separate main homes.
"Married taxpayers with more than one home.
If both you and your spouse owned and lived apart in separate main homes, the limit on the amount of the credit applies to each of you separately. If you are filing separate returns, both of you would complete a separate Form 5695. If you are filing a joint return, figure your energy efficient home improvement credit as follows."
The instructions seem to indicate that both homes need to be owned.
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