As StainlessS mentioned, the requirement is not quite clear, and we can only guess from the script that you have.
However I gave it a try, excuse my newbieness though.
Code:
A = FFmpegSource2("D:\App\youtube-dl\S2_E09_clip.mkv").KillAudio().TFM().TDecimate().ConvertToRGB32(matrix = "Rec601")
B = ImageSource("D:\App\youtube-dl\flintstones.png", start=0, end=100, fps=A.framerate, pixel_type="RGB32")
fdin = B.FadeIn(100)
fdout = B.FadeOut(100)
Afin = A.Trim(200,300)
Afout = A.Trim(300,400)
C = Overlay(Afin, fdin, mask=fdin.ShowAlpha())
D = Overlay(Afout, fdout, mask=fdout.ShowAlpha())
# if you want the image is faded in and then faded out WITHOUT overlay to the video
#A.Trim(0,200) ++ fdin ++ fdout ++ A.Trim(200,687)
# if you want the image is faded in and then faded out WITH overlay to the video
A.Trim(0,200) ++ C ++ B ++ D ++ A.Trim(400,687)
I use 100 frames instead of 29 to display the effect for a longer time.