I am not completely sure what you are describing or asking about. It is completely normal for ARQ to turn itself off automatically during certain situations, backup files automatically and turn itself back on. For example during a WordPress automatic update ARQ does those things automatically. If you are updating a theme or installing a new theme then an ARQ Dashboard message is displayed to you with a link to click to complete ARQ file backup and turn ARQ back on.
What exactly does “refresh the theme” mean?