If you delete a list that is used in a module that contains data, then yes, you would delete the data in the module when you delete the list. However, deleting the list may not be the best approach because we'd have to recreate the list.
Create a line item with the same dimensions as the target you want to set to zero. Set the Format to No Data so that it doesn't take up model space. Then load that (no data) line item into your (numeric) line item that you want to clear. I tested this several times and it seems to work fine.