If you step away from clinical medicine after residency for any period of time, you may find trying to get back in a challenge. Clinical skills atrophy quickly if not used.
And then there's this: I tell my mentees that you learn 50% of what you need to know during your residency/fellowship, 25% in the first six months of your first job, and the last 25% over the rest of your career. So you can see that any atrophy is a big problem.
I'm confused about "you're a PGY-2 in the research track" and "you didn't get an interview with the fellowship". Usually the fellowship in the research track is at the same institution as the residency -- that's the whole point. So you wouldn't be interviewing for anything. If your program doesn't guarantee a fellowship spot and now you're not getting one, that's a more complicated situation -- you'd now no longer be in the research pathway, and might suggest you'll have problems getting a fellowship elsewhere.
Regardless, path forward is relatively straightforward. If you're in the ABIM research pathway, you should plan to complete that locally. try to do research that's proximate / applicable to your long term goals. Consider asking your local mentor if a collaboration with this other site/lab is an option. Once complete, you apply for a position at this other institution. If you're in the research pathway but staying at your home program is untenable, then ask to switch to standard training and apply for fellowship next year -- although you'll need to be prepared to explain that on interviews and you'll have some risk of not getting a fellowship at all. If you're not in a research pathway, then finish PGY-2 and apply for fellowships as a PGY-3. Consider a research year after completing fellowship at the program of your dreams, or just apply for a job.
