Well... to be honest, my personal solution is not to use Eclipse! lol
I rather intellij-Idea, it's fairly more stable than eclipse, but it requires an a little more advanced user.
Java packages, projects, etc are tied up to directories, files, sometimes something changes, a path, or the way the ide scans the dir and your project goes awol. It happens less in IntelliJ than in Eclipse.
Still, one thing that could have happened is you updated (or it auto updated) eclipse or java or android sdk, some path changed, some config was lost and your project lost a link to a jar file, a sdk or the path for something.
That is why usually re scan makes the trick, as it did your re install.