Previously to hide a journal entry in the table of contents app you would remove all dnd5e flags. But since navigation has moved to the the dnd5e flag object it isn't possible to hide those entries in the journal anymore if there is navigation on the pages (Something that is quite useful for organization/navigation).

Solution: Have the table of contents app ignore the navigation object and its keys for the purose of displaying with something like
if ( !flags ) continue; const keys = Object.keys(flags); if ( (keys.length === 1) && (keys[0] === "navigation") ) continue; const type = flags.type ?? "chapter";

Nice addition: Have tocHidden apply to both pages and entries.