[quote=@Andronicus23]
I'm rolling with the concept that there was a pre-evacuation. Father setup a contigency plan and set aside a portion of The Institute's population as "designated survivors". So they had some equipment, supplies, a small synth protection force etc. So they weren't left completely destitute. 
[/quote]

I guess it makes sense that they'd leave little supply caches around in the Commonwealth in case things went south; After all, they could already get a considerable synth presence around, including some spy-bird synths according to concept art.