I think I figured out the issue. When a new version releases, I generally rename it to just “Joplin.AppImage”, to remain compatible with my alias. However, it appears that the appimage launcher caches the previous appimage of the same name, which is launched when the alias is called.
For future reference, if the appimage is integrated using appimage launcher, it must be uninstalled using the context menu before renaming a new version the same.
Thanks for your help @foxmask !