You would have to ask the worms. Some worms, for some unknown reason, like to remain in the lower trays of a stacking tray system. Since the worms can't read the instructions that came with the Worm Factory, they may not all know that they are supposed to migrate up. It is not an exact science. Most worms will move up. Not all will.

And the whole food thing is not really understood by the worms either. They actually munch on the microbes that break down what we call food. In the process the also ingest the "food." If there are still microbes in the lower tray (hint: there are LOTS of them!), the worms will still find plenty to eat down there.

So it comes down to some worms preferring to move up out of their waste in search of decaying organic matter to sip on, while others are content to stay in their own waste looking for microbes there. Some of the smaller worms may be newly hatched worms that have not figured out the system yet.

I am using one of those systems and so far having good luck with it. I am a little confused with your post but thats ok I am sometimes easily confused. What has worked for me is once the first tray is full and the food material is fully engaged remove the top layering for use in the next tray. For me it is shredded paper and a reminants of a sheet of old newspaper. That becomes the new source of the bacterial goodies for the new feeding tray. Add your new bedding and mix that in with some of the old material from the lower tray. Then just add some food to one corner and cover with moistened shredded paper and cover with a solid sheet of paper and moisten that. Within 3 days you should see some activity. Don't feed again until the food is well underway for me it has been around a week or so. Do not add any food to the lower tray.

The worms staying in the bottom tray prefer the wetter/more moist condition. And as sbryce mentioned, there's still lots of microbes there. These must be the lazy worms then.
You might want to move this tray above the new working tray, to let moisture and with that worms move down to where you want them. I remember reading a post about this method. There will still be some worms left come VC harvest time but the poster was quite happy with the result, not so wet VC because there is no working tray above it to leach water down.

Yeah. My bottom tray, full of dark, juicy, 'proper' compost also still housed a proportion of the worm community down there. Still, the tray above was still thriving with wigglers so I removed the 'finished' tray, including the squatters and used it anyway. I couldn't be bothered picking any but the largest ones out and sacrificed the rest as added nutrition for my plants.

So even though this upward migration doesn't always work as advertised, I'm still happy that my worm farm is thriving and still doing its job. Look at it as a sign the worms are multiplying nicely.

One option might be to plonk the worm-riddled compost onto the top (drier) tray and give it a watering which the worms may try to escape from to avoid drowning.

It’s been 5 years since this post started. I hope the worms migrated up by now.

Wasn't there once a nursery rhyme about "the worms crawl in, the worms crawl out"?