If you are using the actual expenses method for home office expense, then the whole house expenses that you enter related to calculating the home office deduction will only be prorated by the size of the office compared to the size of the home. They are not further prorated by using the home office for only three months. You would need to prorate the whole house expenses yourself to indicate that you only used the home office for three months.
If you are using the Simplified Method for home office expense, then the number of months of use is part of the calculation to determine the home office deduction.
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