How can one reconcile "Leave what makes you doubt for what does not make you doubt" with the principle that "Certainty is not removed by doubt"?

The aforementioned Hadith commands avoiding matters whose rulings are ambiguous, meaning those that waver between prohibition and command, so that the accountable individual may base his actions on pure certainty. This is supported by evidence from the Sunnah, such as the Prophet's (peace be upon him) saying: "Whoever guards himself against doubtful matters, he has indeed guarded his religion and his honor." As for the principle "Certainty is not removed by doubt," it means that something remains on its established ruling until it is removed by certainty. This principle applies to all chapters of Fiqh and is based on evidence such as the Prophet's (peace be upon him) saying regarding someone who doubts whether something came out of his stomach: "He should not leave the mosque until he hears a sound or perceives a smell," and his saying regarding someone who doubts in his prayer: "He should disregard the doubt and build upon what he is certain of."