shoot at the shining parts of Clockwerk and dodge all the missiles.

While people say "No" because he blew up as Clock-La, this isn't the case. Their time-traveling, meaning Clockwerk will be alive at that time. Clockwerk almost HAS to be in Sly 4.

yea

You beat Clockwerk at the end of the game.

Clockwerk killed Sly's father by setting a trap that caused the entire Cooper gang to fall into it. Clockwerk then activated a giant crusher, which Sly's father sacrificed himself to stop in order to save his son. The crusher malfunctioned and ended up crushing Sly's father instead.