Are you saying you are playing elite from your pc Xbox app?
Yes. Xbox runs native on Windows 10 via a Microsoft Account and Microsoft Store. Of course, you need to have the "settings" in Windows 10 correct and a Microsoft Account using the same credential set as the xbox account. Most people disable Xbox in Windows 10 and use a "local account" as opposed to letting Windows 10 automatically login to the Microsoft Account. I know I do. I use a local account on Windows 10, but when I first installed Windows 10, I let it login to the Microsoft account one time, so it has my digital licenses from my Xbox accout, Office Products and the Windows 10 digital license in case I need to reinstall these things. Then I switch to a "local machine" account.
I don't know how much of this is needed to make Xbox run on a PC properly, but the Microsoft account and Microsoft Store need to store those licenses for Xbox games and if they are not there, corrupted or not updated occasionally, or you change PC hardware, then you might have to reinstall Xbox games while logged into the Microsoft account to get them to work properly again.
Although I use the Frontier Store bought copy of my Elite game, I installed it over the top of the Steam version so that Steam keeps it updated. I then run Elite manually using the EDLauncher.exe so that I do not have to load Steam everytime I play. I have not played my Xbox version in some five years, but is is available and does run through the Xbox app, although I had to reinstall it when I updated my hardware as well as login to the Microsoft store to get it reinstalled.
In conclusion,, Frontier stores your game state so uninstalling the xbox version and reinstalling it may be a solution for you, but it will not effect your game state, ships, store bought skins or credits. I went through all of this again just recently to get the FS2020 Flight Simulator to install and work and it does run through the xbox app, connect to my Microsoft account and store for licensing.