Yes, I think your right. It's a matter of the Enclave losing it's communication with the west coast. Much like the trouble the Outcasts were having contacting the Western Brotherhood. I also always forget about there war with the NCR.

Yeah, because losing communications with a base isn't ominous? More likely IMO is that Eden and maybe other higher-ups are entirely aware but that it's been classified for the stake of morale.

Murp.

There are a lot of ways to explain Enclave.

1. Not everyone died on the rig. If the Chosen One and his people can escape, I sure Enclave can.

2. Navarro not only base.

3. FO2 designers want you to suspend belief that Navarro is larger than in game appearance. This is a fact for many in game locations, ie there is a lot you as player do not see. Originally both NCR + BoS combined had to take Navarro in a bloody battle. But, in game there not many soldiers there and a crack shot bb gun wielding chosing one can take out with ease. Poof poof poof poof. Ping.

4. There could have been other Enclave or military/political remnants in other regions/bunkers that Enclave scooped up after their FO2 plan failed. Yep, if Enclave plan succeeded those people would be dead, but it didn't.