Pigeon Pete?!?!
 

To this very day, we still have no idea what exactly happened to Pete? Has anyone ever asked anyone in the crew what really went down?

One of two things could have happened.

1. The voice actor didn't want to do the character anymore.
2. They realised the concept was stupid and didn't want to use the character anymore.

Neither of which seems likely since they didn't mind recasting or conceptually stupid characters.

If you want some in-universe explanation... He probably got himself killed doing something stupid.

He last appears in the season 4 finale, Owari.

Although a few episodes before that, Slash said "We don't talk about Pigeon Pete". So I'm guessing that he was kicked out from the Mutanimals off screen?