The last update to beekeeping was a total code rewrite. It would be hard to migrate all of your machines
Plus, the last update just introduced a totally new system for bee mutation where you need to breed different species together for the high tier bees.
You have two options here
1. revert your save to an earlier version of the mod with all of your machines
2. go though the new genetics system to get everything back
I knew people were going to have this problem, but I thought it would be better to just rip the bandaid off