There are so many different penalties and filters and almost all of them are recoverable. Some require you to fix the offending issue and others have a fixed time period that you need to wait to expire.
From my personal experience few people do not even know which penalty or filter is impacting their site. Some websites that think they have lost rankings due to a penalty just have issues with their SEO. You may have just lost backlinks or another division in your company launched a duplicate site. Just be careful not to make assumptions and to properly research your situation. Is it a penalty, filter, seo issue or a combination?