I am going from memory only, so I could be mistaken. But I seem to remember that when the U.S. military learned of LHO's "defection" they changed all the friend/foe identification codes that aircraft used when approaching U.S. controlled air spaces. Those codes were supposedly considered the most sensitive information that LHO might be able to share with the Soviets. By changing those codes, they believed that they eliminated the main threat that LHO's defection posed. I would think it would be prudent to change those codes routinely every so often anyway, regardless of any potential leaks. So, I suspect this wasn't a big deal to them.
Yes, the "assistant operations officer" of Oswald's unit at the time, John Donovan, said they had to change all of the IFF codes. But they would do that periodically anyway.
WC testimony:
Mr. DONOVAN. I recall that he got a hardship discharge. We offered to get him a flight---that is a hop from El Toro to some place in Texas, his home. He refused. We considered that normal in that if you take a hop you sacrifice your transportation pay. We offered to take him to a bus or train station. He refused. But that is not particularly unusual, either.
I recall that he was gone for some period of time, and shortly before I got out of the Marine Corps, which was mid-December 1959, we received word that he had showed up in Moscow. This necessitated a lot of change of aircraft call signs, codes, radio frequencies, radar frequencies.
He had the access to the location of all bases in the west coast area, all radio frequencies for all squadrons, all tactical call signs, and the relative strength of all squadrons, number and type of aircraft in a squadron, who was the commanding officer, the authentication code of entering and exiting the ADIZ, which stands for Air Defense Identification Zone. He knew the range of our radar. He knew the range of our radio. And he knew the range of the surrounding units' radio and radar.
If you had asked me a month after I left that area, I could not have told you any but our own. Had I wanted to record them, I certainly could have secretly, and taken them with me. Unless he intentionally with malice aforethought wrote them down, I doubt if he would have been able to recall them a month later, either.
Mr. ELY. You recall that various codes were changed. Now, at what level were these changed? Was this an action of your specific unit, or a fairly widespread action?
Mr. DONOVAN. Well, I did not witness the changing in any other squadrons, but it would have to be, because the code is obviously between two or more units. Therefore, the other units had to change it. These codes are a grid, and two lines correspond.
And he gives the grid that you want, and he reads back "AB," or whatever the reply is supposed to be, the authentication is supposed to be.
Mr. ELY. Are authentication codes changed from time to time as a matter of course?
Mr. DONOVAN. They are changed from time to time, that is right.