I've been having to contend with this issue for several years now. We create second level menu items to go into the mega-menu drop down. Within the Helix options, we drag and drop the menu item within the mega menu. Unfortunately, these items do not immediately apear. We clean cache, resave the menu item, try moving it into different places, but it won't show up on the front end for at least fifteen minutes to maybe a half an hour.
Needless to say, this causes frustration for our client.
We're using Helix Ultimate 2.0.18 on Joomla 4.4.4