The classpath for a project is stored in the .classpath file in the main project directory. Eclipse won't show it to you, you'll need a file manager (i.e Windows Explorer) to see the file, but you can edit it with a text editor. Most likely the file got corrupted and somehow at some point was "fixed" - usually making a classpath change in Eclipse causes Eclipse to rewrite the file based on its internal data.
When Eclipse screws up (which it does often, depending on what you do with it), there are usually several things you can try to restore order. You don't have to do all of these, bout one or a combination of a few of them usually gets me back on my feet.
1) Backup the current project (using Windows Explorer) then in Eclipse delete and recreate the file. Then in Explorer copu over the source files again. This is made extremely easy if you follow a directory
pattern such as that enforced by
Maven - just copy the src directory. Then in Eclipse, refresh the project. 9 times out of 10 this is all it takes. (This takes care of Eclipse screwing up the .project or .classpath files or the .settings directory)
2) In Eclipse create a new workspace. Then follow step 1 to recreate the project. This usually fixes the other 10% of the cases. (This takes care of Eclipse screwing up something in the .metadata directory within the workspace.)
3) Reinstall Eclipse. This usually helps only if a plugin keeps configuration files and the like in the Eclipse installation directory. Plugins aren't supposed to do that, that's what the workspace/.metedata directory is for) but I've seen too many plugins that don't follow this simple run (we are stuck with one such plugin at work).