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The error message is indicating that existing data is violating the UNIQUENESS and it will not enable it.
Here are the steps that will help troubleshoot
1. You will have to identify the same LOT# spanning multiple distinct items, maybe write a sql query
2. Once you find the LOT# remove inventory so only single item is tied to this lot. Misc issue out can help remove the un-needed inventory.
3. Retry enabling the LOT setup and hopefully you will not get the error message.
All the best. This is not an easy task, make sure you try it in a test env. first.