So I found this article https://accountants.intuit.com/community/lacerte-tax/discussion/03/302

When a client had a renter in their primary residence and then the renter moves out, we need to retain the historical depreciation for eventual sale (if they sell before death and step-up in basis).

Based on this article, when I delete the Sch E, change screen 22 method to 99 to not calc more depr, suppress the critical diagnostic to e-file, and let these assets sit forever? Do you take it out of Lacerte and keep a note in your perm file? How are the rest of you handling this?