The files with ~ are ignored by the IDE by default and are not visible. If such FileObject is renamed (through an code), its visibility is changed correctly, but it's not reflected by the IDE.
In PHP there is an action that downloads files from an FTP server. The downloaded file is saved into a folder that is opened in the project explorer and the new file is saved for example as index.php.new~ . When whole file is downloaded, then the file is renamed to index.php. The problem is that the appropriate node is not displayed in the explorer after the action.
When I remove ~ from Tools->Options->Miscellaneous->Files->Ignored Files Pattern, that the download action works correctly. So it looks like the change of visibility is not reflected in the explorer.
This works in NetBeans 6.9.
See issue #195141
According to this test the filesystem changes are correctly reflected in nodes (and thus explorer):
Integrated into 'main-golden', will be available in build *201102160501* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
User: Jaroslav Tulach <email@example.com>
Log: #195297: Verifying that change in visibility is reflected in FolderChildren