The Impala is missing in action for much of season 7 as Dean and Sam are forced to put her in long-term storage to avoid FBI detection. Near the start of the season, Leviathans impersonated the Winchester brothers and went on a killing spree, putting them at the top of the most-wanted list.
The Impala is further damaged when Crowley and his demons attack Castiel. While Dean and Bobby take refuge in the car, it's flipped onto its roof and has all its windows blown out by the demon onslaught. The Impala doesn't stay damaged for long.