Toggling the states of event flags works quite a bit different for Sword & Shield when using PKHeX. The usual event flag editor isn't available for SWSH save data, so what we can instead do is toggle save data blocks!
Access the Save Block Editor by navigating to: SAV > Block Data
You should be greeted to a window that looks like this:
You're almost done! Included below is a table full of notable flags that I've collected that may be useful for a lot of users.