There was a big bug in a couple of the earlier releases of version 0.54:
when we passed your plugin list to an external library we use, if the loadorder was severely broken (eg. "unofficial dawnguard patch.esp" set to load before "dawnguard.esp"), it removed all the content from your plugins.txt file making it blank.
We didn't expect this extreme behaviour, nor we thougt about testing such extreme cases, our fault and we're sorry for any inconvenience and headaches this might have caused you.
What happens after you're affected by this bug is that all your plugins will turn disabled, they're still there, in the same load order as before (well, a bit better, cause the broken elements are automatically fixed by NMM), but you'll need to re-enable the ones you want active by going in the NMM Plugins tab.
Version 0.54.10 and higher should have fixed this issues for everyone, so you are safe to use them.
Keep in mind that this issue was caused by plugins that were broken (eg. ._Pulserifle from the Alien Weapons mod, or a broken esp patch), the manager will ignore these files for the time being.