Reusable workflows are slightly more tricky to remove from the SharePoint UI than the list workflows. In SharePoint Designer, the main way of managing workflows is in the Workflows section. This may well tempt you to remove the workflow simply from that list and be done with it. This, however, will not remove it from the SharePoint UI, and thus an old depracated workflow is still available for users.
The right place to remove the workflow from is to open the All files section, find the Workflows directory there and delete the whole workflow directory.
But what if you already deleted the workflow in the Workflows list and now you have no directory for it anymore but it still shows up in the SP UI? This is what I was researching this morning. The place to go in that case is - surprise surprise! - the _catalogs directory. There you will find a folder named wfpub. And in that wfpub folder, you still have the directories for even those workflows that were deleted from the Workflows section listing. Delete these directories with all their contents and you're good.