This is a painful bug for audio, because many times we are replacing hundreds if not thousands of files this way.
Import 5 soundwaves into a project, and save them.
Import those same 5 soundwaves again into the same location.
When prompted with the Overwrite dialog, click Yes to All.
The editor will overwrite only one file, and then present the Overwrite dialog again.
Trying No to All will yield the same results.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-40164 in the post.