The problem is that the drug doesn't stay at an effective level in the body for 40 days (it also takes more than a month for the drug to take effect), and the consequences of allowing lupus to flair include accumulating permanent damage to, for example, heart, lungs, kidneys and joints. Additionally, there's no good information yet on how an immunocompromised patient in a flair will react to coronavirus infection, beyond the general notion from our rheumatologist that putting your malfunctioning immune system into a state of dysfunction and then getting the virus that puts your immune system into a state of dysfunction is probably really bad.

source: my partner has rheumatoid arthritis and takes hydroxychloroquine, and we've been concerned about exactly this sort of thing happening for a while now.