I well remember this happening to one of my one-time favorite series, Robert Asprin's Myth Adventures. The early books, with real villains and consequences, were the strongest. But soon, the resolution to every book was just "let's ask them to join the team!" With that said, the overall problem of a book where nothing is ever at stake isn't just found in comedy. Writing is a ruthless art, and if you aren't willing for your characters to suffer, it shows. This is especially a problem in comedy, since bad things happening to the characters can bring down the happy mood (unless you're writing really bleak comedy).
One approach to avoiding this is to do a loose parody of an original with a strong plot but little humor. A really well done parody of this type (Airplane!) can rival or even surpass the original. Another solution is that the characters can experience minor events as major disasters. Think of the comic strip Peanuts. Plotwise, nothing ever happens in the strip, but from the perspective of the characters, heartbreak, humiliation and catastrophic failures are daily events. Similarly, in the movie The Devil Wears Prada, the title character doesn't hurt, kill, or destroy anyone, but she still serves effectively in the role of villain --it's all psychological.
In summary, don't write a comedy book --write a substantive book, and make it funny. That's how Terry Pratchett managed to keep it fresh over the course of a very prolific and successful career.