I've been experiencing the same issue. I have no planted berry bushes, however I do have water extremely close to the nest. They were name-tagged, so there is no way that they should have despawned, and there are people running in and out of my base 24/7 (I run a server) and nobody has reported the bees coming anywhere near my pond at any point. I moved them over from where I found them with silk touch, and there are no other nests for miles and miles, so they couldn't have just migrates nests. For now, I'm going to put the remaining bee's nest away until the next update. Hopefully this is fixed soon!
Phoebe Woods
I've been experiencing the same issue. I have no planted berry bushes, however I do have water extremely close to the nest. They were name-tagged, so there is no way that they should have despawned, and there are people running in and out of my base 24/7 (I run a server) and nobody has reported the bees coming anywhere near my pond at any point. I moved them over from where I found them with silk touch, and there are no other nests for miles and miles, so they couldn't have just migrates nests. For now, I'm going to put the remaining bee's nest away until the next update. Hopefully this is fixed soon!