Use REPLACE mode. This button may not be on your Transport. If not, Right-Click on transport to customize, and add the Replace button (near the bottom of the Modes and FUnctions options on the right).
The button is a big X that gets Orange when active - super handy. As long as not Take folder already exists, it will overwrite any audio regions (though not destructively removing the audio from disk). However, if a Take folder already exists, Logic will not replace but will behave as if Replace were not on.
Same rules when in cycle mode.