My bees are not producing while the Upgrade:simulator is installed, even tried using time in a bottle on the beehive and it did not produce anything. If i take the upgrade out it works.

Did you put the 'flowering' block (or feeding slab with multiple flowering blocks) in front and one below of the beehive?
Mine is like this and works fine:

possible Solution: are your non productive beees nocturnal?

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