This is certainly an OS level problem. The way custom software-level shortcuts are saved are by putting them into each individual program’s .plist file, where it stores its preferences. There are some implications of that to be aware of, such as if you ever delete the preference file as a troubleshooting step, you lose your shortcuts. Likewise tools that do “clean” uninstalls by wiping related configuration files when moving software to the Trash will also wipe shortcuts.
I’ve never seen shortcuts just get lost without an accompanying loss of all preferences for that software though. So it might be good to check and see if that’s happening as well.
If not, my off the cuff guess would be some level of breakage somewhere in the Mac’s somewhat complicated preference caching system. Unlike in the old days when the .plist file was the final and full authority on settings, these days it’s almost more like a disk-based backup of your actual preferences, which are themselves in an infrastructure that users don’t really have direct control over. I’ve even seen cases where if one deletes the .plist file while the software is closed and launches the program, all of their old settings come back because the .plist isn’t even being checked for by the system. You often have to reboot, log-in, or run a command-line script to cause the preference caching system to restart itself.
In short, you may be in for some Apple troubleshooting if shortcuts are selectively disappearing from .plist files, that’s a very weird bug if that is what is happening. My first hunch though would be to check for third-party “system cleaning” type utilities, and maybe doing a safe boot reboot cycle to flush all of Apple’s caches and have the system rebuild its concept of what is on the disk.
By the way, this and many other reasons are why I’ve largely abandoned using Apple’s keyboard customisation system. For one thing I don’t like how they are tied to the .plist file because deleting that file is such a common troubleshooting step on a Mac. I ultimately went with BetterTouchTool for 100% of my keyboard customisations. The only real downside to using them is that, as a dynamic override happening “above” the software level, they don’t change in menus. The menus always go on showing the default shortcut.
Plus, it’s a great tool anyway, as your shortcuts can do so much more than just firing off one menu command. Better shortcuts are only one small thing of what all it adds to the experience of using a Mac.