The "Intersect" program is coded such as it deletes itself either during, or after run-time. As we have seen on several occasions when Chuck, or someone else (e.g. Shaw), has used Intersect computers or glasses, the monitors/glasses have been left in a state where they have either been black (disabled or just inactivated) or displayed the text "Upload Complete". This combined with the fact that everyone have treated the equipment as nonfunctional after it has been used hints that the program is only good for one upload.
This is actually confirmed later on in the show (S05E01, "Chuck Versus the Zoom") when Chuck and Ellie are standing down in "Castle", looking at a pair of glasses;
How certain are you that these glasses only had one reload left in them?
Like, very certain... I tried to access the program, but, there's no way to update it. This version of the Intersect is a one-time deal. I'm sorry.