Just save any of the projects from the workspace directory that you want to retain, delete the decompressed files and directories, and unzip or untar the Eclipse download again. After replacing the saved projects in the workspace directory (omitting any suspect projects that might have caused the problem in the first place), you’re set.
One reason people like Eclipse is because they have control over the (re)installation process. This is in stark contrast to other IDEs, some of which are massive and do so many things behind the scenes that you can never trust them.
Note that you also can migrate projects from one version of Eclipse to another simply by copying project folders into the new version’s workspace directory. This doesn’t always work with major revisions of Eclipse, but with minor revisions, it works like a charm.