Bees can be transferred from one colony to another. This is particularly useful in weaker hives that may need additional support from more worker bees. Transferring of bees however is generally done by humans managing their hives. Bees generally will not voluntarily go into another hive. Typically the only time bees enter other hives is to rob weak, often queen-less, hives of their honey stores.
I imagine what you are experiencing is a population in boom in one of you top bar hives. Most likely a large number of pupating brood has recently emerged from their cells and you are now witnessing a thriving colony of bees. The other colony sounds like it may be having a little bit of trouble.
I would think about expanding the space of your larger colony if you have not already done so by adding some additional top bars. This is especially important if you notice the majority of the comb is filled with brood, and food stores. In your smaller population hive you may need to downsize to not overwhelm your bees.
I would make sure in your other hive that you still have an active laying queen. It is possible that that colony may have swarmed (although more unlikely do to the age of your hives). It is also possible that the queen is either not laying well or is not longer in the hive (may have died or been killed). If you do not find evidence of freshly laid brood or cannot locate your queen you will need to requeen. I would also look for any queen cells (peanut shaped cells) to see if the workers are rearing a new queen, that would be in indicator your queen is no longer in the hive. You would also not need to requeen if they are rearing a queen.
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