I have used the recent facility to add custom menu entries to the Dashboard as explained in Setting up and using a custom menu in QuickBox
It worked well, but after updating QuickBox (using “Run updater” from the Dashboard) the new entries are gone, and custom.menu.php has been restored to its original content.
Could you have a look?
Apologies for this. Thank you for bringing it to our attention. I’ll give a look soon.
Had the same issue for my FreshRSS custom menu when updated the QB.
Just a reminder 
Looks like the updater is not honoring the .gitignore file. I’ll have this polished up tonight. Thanks for the reminder! 
###EDIT:
You should be able to pull the update through the QuickBox dashboard updater. The overwrites should no longer be an issue for those select custom files.