Yes, If you have assets that remain on the books when you sell a property, you will have to close each one of them out individually. If you dispose of an item the value goes to zero. If it was purchased with the property, a portion of the property cost would be applied to the asset.
The 1099-S is an information form. If you make adjustments to it it's okay, but be sure to document why you made the changes. That is always the Key when the IRS has questions.
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