Summary: I used a tool enchanted with silk touch to harvest a bee nest immediately after watching two bees enter the nest. When I placed the nest in its new location, there were no bees.

I haven't tried to reproduce this, but here are the steps I took to get to this state originally.

Map world seed = 1291376329743018843

There's a ruined portal on the surface at X:243 Y:66 Z:-249. I looted the chest, which has a golden shovel enchanted with silk touch.

I headed to X:319 Y:70 Z:-264, where a bee nest is located.

I cleared out some leaves in front of the entrance, after which two bees flew out.

I waited until both bees were sated at nearby flowers and re-entered the nest.

Then I used the silk touch shovel to break the nest. The icon said merely "Bee Nest" when I grabbed the nest. I thought it was supposed to have the count of bees, but I didn't pay much attention to it at the time, thinking it was probably just a labeling issue.

I grew a tree back home and placed the nest. There were no bees. I waited several game days to be sure; no bees.