I have about 3000 folders with 160,000 photos. I just dicovered that some of the folders that contain pictures do not have a .tonfotos.ini file. I have identified at least 30 folders without the .ini file.
I tried to re-index them as you described elswhere but that did not resolve the problem.
I am using Windows 10, 32GB and SSD hard drive for the photos.One main folder with multiple sub folders.