Hello Samantha,
Yes, in the scenario you described this is standard Business Central behavior. Zeroing the inventory can allow you to change the Base Unit of Measure, but it does not remove the historical Item Ledger/Warehouse Entries created using the old UOM; deletion of the old Item Unit of Measure is subject to a separate validation, and the standard Item Unit of Measure table includes the CheckNoEntriesWithUoM() validation specifically for this purpose. So I would recommend leaving the old UOM on the item and simply making sure the new UOM is used as the Base/Sales/Purchase UOM as required rather than trying to bypass the standard validation or delete historical references. Microsoft also confirms that the Base UOM is the basis for how inventory quantities and alternate UOM conversions are maintained.
Regards,
Oussama Sabbouh