I wanted to create an additional report but maybe this is related to being unable to save some things.
So here it goes (reproducible):
select any element with the colour set with the global swatch, press edit the swatch, change the colour, save. Either exit the designer or publish your site. Changes will not be saved nor published.
To make this work correctly first you need to remove the global swatch from the object, then select and edit swatch - no idea what’s the difference under the hood between these two flows.