Yes she will have to go back to CFO cebu for the stamped once she have the visa.

Here's the address:

CFO Extension office (for CFO pre-departure registration and stamp):
Causing-Lozada Building.
Osmena Blvd. corner Lapulapu St. (near Plaza Independencia). It is located on the 2nd floor in DFA building, not far from Basilica Minore del Santo Niño.
CEBU CITY
Phone & FAX: (63 32) 255-5253