Subscription import seems not very reliable in NewPipe. Half of the time import just doesn't work and doesn't even show any errors or anything. My guess that's the reason you don't have your subscriptions. Because they were not imported correctly.
Anyways, I think you'll be better off not using NewPipe subscriptions at all. Because there is no way to export them and merging multiple imports is very problematic. I recommend you using RSS feed from Invidious (make sure you use multiple instances for your RSS feed or you gonna get errors) or Piped (you need account to use RSS) and some sort of RSS reader (I use Flym).