I wouldn't rush off to do something I'm told on the internet unless I'm absolutely sure it's the right thing to do for my bees, nor would I act instantly on something I'm told over the phone unless that person has seen my bees for themselves - one person's description doesn't always match what another person thinks is being said.
I can't say what I would have done, because it's hard to work out exactly what you've done from your first post, but it looks as if you've got an older queen in a nuc as well as two other colonies/hives you expect to raise new queens. You've seen open queen cells and have assumed the newly emerged queens are still there, although you haven't seen them, so have removed all existing queen cells and let somebody else take them away. It might be worth making sure at least one of those new queens is kept safe in case you need her.
Yes, in some cases a newly emerged virgin queen will be only slightly larger than a worker.
When was the last time an experienced beekeeper looked through your hives with you?