It's pretty common in film, TV and even theatre to have several versions of the same puppet, each built for specific effects or sometimes because of costuming requirements. Usually you have one or more "hero" puppets that are used most of the time and then others built so they can perform specific actions or be used to create a certain effect.
For example, for the web series I'm doing there are a bunch of cockroach puppets. Three of the cockroaches are "hero" roaches and have fully articulated mouths and heads that pivot (they're operated by rod controls). Other "background" roaches just have heads that pivot because they only appear in the background of shots. There are a few stuffed "stunt" roaches that have full bodies and legs and can be thrown around on the set. Still others are specifically built so they can be rigged to do things like drive a tank, kayak, rollerblade, etc. and eventually I need to build one that can be radio controlled.
Some shows that use a lot of flocked or animatronic puppets will have several versions of the character so that when one needs touch ups or repairs they can just switch puppets and keep shooting. On CBC/Nick Jr.'s Nanalan' they often have to rotate 3 versions of each character because the flocking requires frequent touch-ups - while one puppet is on set being shot, one is being touched up and another one is drying so it's ready when they need it on set.
I know with the Muppet productions it's not uncommon to have 5 or more versions of a puppet - I think they had 10+ Piggy heads for Muppets From Space and something like six or seven Pepes.