How bad is the problem? Can you post some screenshots?

If it's not that bad, and limited to few frames per episode, you can leave them "as is"; probably no "normal person" (read: most of all out of this forum) will note it.

If it's bad, but still limited to few frames, you could always modify the replaced frames to remove logo.

If it's bad, and with a lot of frames to fix, you could always try some de-logo script; even if they are not perfect, they work very well on animated material; or, make the "patchwork" job, to replace the logo with the non-logo'd part...