San Francisco now requires conditional use approval (via hearing by the Planning Commission) for the removal of both authorized and “unauthorized” (i.e., unpermitted) residential units, under Section 317 of the Planning Code.
Ordinance 33-16, modifying Section 317 of the Planning Code, follows (and repeals) Ordinance 23-16, requiring conditional use authorization for removal of authorized and unauthorized units in the C-3 (Downtown Commercial) District.
You can read the full text of Ordinance 23-16 here and Ordinance 33-16 here.