Schematic <--> Layout Synchronization

To begin, I am a student using the OrCAD/Allegro 16.2 design package to modify the "BeagleBoard-xM" design for our specific project. I am having issues with my design. An original schematic (OrCAD Design) and board file (Allegro PCB Design) were provided for the project I am currently modifying. Using these two files, I needed to remove select components and signals from the original schematic. When I began, I removed each component and signal on the schematic, but no changes were updated on the board file; therefore I went through the board file in Allegro and deleted each component based off of the changes made in the schematic.After presenting the changes to the professors who are advising, they said that our design will not be accepted unless we can synchronize the ORIGINAL schematic and board file, so that, when a component is deleted in the schematic the component is simultaneously removed from the layout and the board file is updated. 

 How can I go about doing this properly? Are there are tutorials available? If possible, could someone help me out and guide me through the process so that I can re-modify our design as quickly as possible? I can be available through email or phone.

 Thank you.

Kyle