One of my clients is running into this issue, where when they imported a new .xlsx file to modify the item library, the inventory/stock count is not re-counted when the value is set to 0 in the new quantity column.
Here is an example:
|Token||Current Quantity||New Quantity|
An interesting finding was that, when the value in the new quantity column was greater than 0, the item inventory/stock was properly updated. And these items in the example definitely had inventory tracking enabled, since their current quantity were already above 0 in the first place.
I am not too sure what other info I should provide other than the token numbers, but please let me know if you anything else to proceed with investigation.