Depending on what is selected in Setup > Timesheets & Hours > Preferences determines how the hours are restored (more information here). The section, Project, Task or Issue Deletion Preferences, offers two options:
- Keep logged time already added to timesheets as general time: If a project is restored at a later time, the time remains on the timesheet as General Time. This is likely the setting you have selected.
- Delete any logged time: If a project is later restored, time already logged is restored to the project. You may want to consider changing to this option instead for future projects.
As for the project that was already deleted and restored, those hours will stay under the General area of the timesheets. You can re-log the hours on the Project, however, that will require a little bit of manual work.