Suppose that the C partition is the system partition.
1. Start windows "CMD".
2. Run "bcdboot c:\windows /s c:" => This means copy the boot files into partition C.
3. In diskmgmt.msc set partition C to active partition.
4. Reboot the system.
Then you can delete the hidden partition.
Note: When there is a hidden partition exists, You can't install Ubuntu in windows.
It will prompt a warning like : "Could not find Ubuntu/installation.iso".