This annoying little quirk also caused my file to stop showing up in the "open resource" dialog.
It happened when I accidentally dragged the java file into the "gen" folder. I guess the SDK automatically marks anything in there as derived.
Derived just tells the Eclipse IDE that files were generated by the system, and will be overwritten if something else changed.
To remove it, simply right click on the file and select "Properties".
From there, untick "Derived" and then save it.
Now, back to business!
