The best will be to get rid of this logo; you could try to cancel it somehow, using an avisynth script (or some other method) but result will be less then perfect; or you could use the source without logo, OR... you could try to use the source with no logo as a "patch" to cover the logo... it's a hard task, but could save a lot of time; I have done it with Supernova, and results are perfect, but in your case, with blended frames, you have to test it...
Good luck!