Hi Huiying,
There are 2 sources of database information, one containing information about all the projects (usually located in <home directory>/Phenix), and one for each project containing information about the project (the one you found located in the .phenix directory of each project). Were you able to recover the database about all the projects (<home directory>/Phenix)? If not, you can import each project into the GUI to rebuild that information. To do so,
1) Select "Projects" from the top menu bar
2) Select "Import project" from the menu
3) Provide the root directory of the project. This would be the directory above .phenix (e.g. <project directory>/.phenix).
If your .phenix files for each project are corrupted, this will not work. In that case, let me know and it may be possible to rebuild those files manually if only certain files got corrupted Thanks!