I have been looking through the DB and a few years back I saw that the VA Medical Center in Omaha, NE has a license listed and now it does not. Is there any way to search that up or is it lost forever?
It is unlikely the VA Medical Center would have ever had a license that you would have found in the Radio Reference License Search, since the Federal Government operates in their own bands and does not issue licenses to itself (at least that the general public can see, but its not maintained by the FCC).
I do see that the VA Medical Center in Omaha was last seen operating a Conventional frequency with P25 Voice:
When searching the license section for non-Federal licenses, you can always click to show Expired Licenses, which should give you a decent amount of history (for however long the FCC maintains that historical information):