Troops can be changed for a few reasons but the primary cause is troop balance in the game. Weekly updates and major patches can and often do include some changes - because of troops under-performing, abusive strategies emerging, kingdom overhauls, bug fixes, etc. Be sure to check for any such changes on the homepage and/or the community forum.
Troops that have been changed for the worse ("nerfed") are typically eligible for a Refund. This provides all players with the option of refunding any such troop for the total souls and traitstones that went into upgrading it, such that they can be put to use elsewhere if desired.