Likely the files that are "missing" are being filtered from the project explorer.
The project explorer is a highly cusomtisable viewer and many plugins provide filters and content providers.
The filters and content providers can be turned on / off via the project explorer's context menu (right click in the top right corner of the view).
Select 'Customize View'. Then in there you can try to turn off individual content providers and check if your missing files become visiable.
It could be that the files being filtered is uninintentional (i.e. a bug). Once you know which content provider or filter is responsible you may consider either
- peramanently disabling that filter
- filing a bug report against the software that provided this filter
I any case, the first step is determining which filter is responsible.
Kris
Kris De Volder -- SpringSource