Hello nath.bod,
saveReference operation is applied to the active frame, so you need to switch the frames in your script to save the information for each of them:
path="e:"
for i in range(len(chunk.frames)):
chunk.frame = i
file_name=os.path.join(path,str(i))
chunk.frame.saveReference(file_name, Metashape.ReferenceFormatCSV, items=Metashape.ReferenceItemsMarkers,
columns="n,[u|v|w],")
Let me know, if it works as expected now and gives the desired result.