I originally thought you were asking how to sync cues and grid data back to your main library from the USB - which, although I've never done - I'm 100% sure you can do.
But I'm not sure what you're asking - if you update your cues/grid in Rekordbox - then when you sync to the USB, the updated cues/grid will sync.
If you update on a device (eg CDJ), the updated cues/grid will sync back.
So I'm not sure what the issue is - in that scenario - both the main library and USB both have the correct cues/grid.