I believe I am also having this issue. I may have some information on how it happened, but not why.
Within the theme customization page, under ‘Layout’, I had my ‘Primary Navigation’ settings all set up with a logo. Then, under ‘Site Identity’, I clicked and un-clicked the ‘hide site title’ checkbox. At this time, I lost my main navigation and the logo. I am now unable to recover it.
Any ideas? Thanks.