Sorry for the delay in response, Benji. Forgot to follow up my post for a few days.
First, once you're in the program at this point, you can only take a somewhat philosophical view of "taking things as they come" because worrying too much about your future will just give you an ulcer. You will want to make decisions that will most prepare you for any eventuality. So buff your CV/grades to make sure you are competitive for civilian programs. If you want to do a fellowship, keep working toward that goal but realize it may not come as quickly as you expected. Be flexible.
No, I'm not IM, but as yet, few residents really know what will happen to any of the programs, because the muckity-mucks above us haven't figured it out yet. Residencies in the Air Force are an endangered species as far as I can tell. The integrated forecast board comes out in June/July so we'll know soon how quickly slots start disappearing. I think your concerns are valid regarding the potential for a "lame duck" residency. As I understand, some AF staff will be moved to Brooke Army Medical Center (the army hospital here in San Antonio), essentially creating a multi-service hybrid, but I am not sure that there is a plan to move AF GME slots over there as well. Even if they merge residencies, I can't see the same number of resident slots in the combined program as are in the current separate programs - there's just not enough clinical volume, even after Wilford Hall closes its inpatient facilities and patients move to BAMC.
As far as I can tell, morale is at an all-time low. Not only are few of my staff physicians happy with their case-mix and patient loads, now they are working in an inpatient facility that will soon cease to exist. If you only have a four-year commitment, I would push hard to defer to a civilian residency. Military or not, as a general rule of thumb, you want to train in a residency program that is stable, moving forward, and filled with mostly happy people. If you have a longer commitment (like myself), the decision may be a little tougher. I am fortunate because (a) I am more than half-way through my residency and (b) my program is combined with a civilian program in town so that I am actually doing 80% of my training at a university or otherwise civilian setting, and my training is not suffering too much.
There are still many good aspects to training and working in the military - your colleagues are decent people with a strong sense of integrity, patients are almost universally appreciative of the work you do, and the pay is nice. Service to the country, as cliche as it may sound, is still a noble choice in my opinion, regardless of the aforementioned perks. It is just frustrating that the choice is coming with more strings than expected.
Disclaimer: I am one resident whose opinion is informed by his own professional goals, disappointment in the downward spiral of Air Force medicine, and constraints imposed by his payback time. You need to talk to other residents as much as possible, especially those in IM if that's your planned field, and get a broad opinion. I can't guarantee that my opinions reflect everyone else's, but they are fairly consistent among all of the residents in my program. If you have further questions, please feel free to contact me through my profile. Otherwise, good luck.