I have designed a similar application.
I wrote a separate server application that makes data acquisition/storing/server. This app has no user interaction except the front panel showing its current status. It runs 24/7.
I also wrote a client application that takes care of all user interactions for data display and config. Data is retrieved and config is set through requests to the server app.
Splitting your app in server/client parts maybe more or less easy depending of how both parts already communicates in the application. If you use a lot of different communication mechanisms (globals, queues, LV2 globals, etc) you'll have to convert all this to VI Server calls.
This offers a lot of advantages as the client application can be
eventually run from anywhere on the LAN/Internet instead of being run on the machine connected to the instruments. But I think it is already what your actual client application does anyway.
Good luck.