Ah.. I thought you were talking about the Android box shortcuts on the home screen (and the folders on it.)
What version of Kodi are you running?
I'm guessing that it's 15.2 as you have 'set shortcuts' presumably from the installation that the manufacturer did, right?
If you are running 15.2 then to have a faster running Kodi and a more customizable one, to boot, you'll have to uninstall it and re-install version 16.1 from the Google Play Store.
You won't be able to save your settings if you do this, but I'm assuming that this won't be an issue.
(The versions look the same but there are a lot of good changes 'under the hood' so to speak.)
I don't know why your custom shortcuts revert back to the stock installation version, but I'll bet that this issue goes away with the fresh install of the newer version.
I bought one of these boxes, too, and Kodi 15.2 performed irrationally for me, as well.