After some experiments I managed to change Saints HQ status from mission scripts and Sandbox+:
-- Set Saints HQ to Level 1
city_chunk_swap("sr2_ug_chunk104_ST_HQ", "level1", false, true, false)
-- Set Saints HQ to Level 2
city_chunk_swap("sr2_ug_chunk104_ST_HQ", "level2", false, true, false)
--...