We are seeing some users that are getting issues with their blockchains being corrupted and then having to perform a full resync from scratch of the same.
The proper way of shutting Agama native mode is not by pressing the Quit or X exit button on the program's selection tab.
As shown below the correct way of doing it would be selecting the Stop option inside the tab menu next to your coin icon.
Only after this you are good to go and you may proceed on closing the program.
You as a user need to be aware that this is not the proper manner of closing Agama native mode. In this way, you will stop having errors and will be able to use your same saved blocks with no type of error or corruption on your database.