It doesn't sound like it's really a matter of what flexdashboard can do, it's more of question of how you link the data to your flexdashboard. If you're collecting data into files, then periodically making those files available to your webserver, that isn't very live. But the more you automate that, the more live it can be. If you can get data every few seconds, you can use reactive polling:
https://shiny.rstudio.com/reference/shiny/latest/reactivePoll.html
to update plots, etc. on your dashboard.