Removing logo from a certain period

[mach3]

Hi!

I'm using VirtualDub and MSU Logo Remover filter together. When I have to remove a logo from a clip that contains the logo "all the time" (every frame) they work very well.
But how can I remove a logo from a clip that contains that logo just for 1 sec? I do not want to filter the whole clip, because the logo's size is big and it will be ugly.

[Digitalboy]

If its only on for a 1 second is it worth making an effort to take it off? Maybe you can crop it out but thatwill require losing 1 second.