The total of all your properties income and loss is summed up on Sch E. If you have a gain, it goes to your income. If you have a loss, it is limited to $25,000 or less, based on your income and filing status. If your income is high enough, you will just keep carrying the loss over until you sell or have lower income.
The total carryover will accumulate in the program but you need to track each property and its loss separately.
Reference limitations here.
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