How to make deletion of hotkeys more consistent

What operating system are you using?  There used to be a Permissions issue with some OSX versions a while back.  It could be that your new settings are not saving when you close Photoshop because the relevant file is read only.  This was a good while back 

Preferences folder read-only error | Permissions issue (adobe.com)

Do you shut down Photoshop correctly when you close it?  When systems crash and Photoshop does not shut down properly current settings are not saved.

Do you use custom workspaces?  If not, try setting one up, and check to save custom shortcuts toolbar and menu.  This is a very handy feature as it allows you to make context sensitive shortcuts, and still have access to the defualt shortcuts by switching to Essentials workspace.  

What hotkeys are you using for your Actions?  It has always seemed to me that the Function key shorcuts are far too valuable to waste on their defaults.  I suspect very few people use many, if any, of those default settings, and that would especially true if they have plenty of screen space.  So I use them to do things like switch workspaces, toggle Lazy Nezumi presets, invoke a sharpening action etc.  Doing those things with a single key press can greatly streamline your workflow.

Are you saving your hotkeys as a custom keyboard set?