We by default don't track inventory on special order products because there usually isn't any. If you turn on inventory tracking you see that fake stock value of 9,9999. To reset this in bulk, first go to products and sort by inventory.

Next select all the products that show 9,999 or the whole page depending on how many there are. Then click Bulk Edit.

The next page you will select Columns, then click Track Quantity.

Then you can turn off Track quantity by deselecting the checkbox.