Physical Count for individual items

I currently utilize a modified physical count that allows me to enter a startin and ending location in a flexfield to generate a count within the boundaries of the starting and ending locators. My issue is that when I have completed counting my storeroom which has about 150,000+ SKU's I have to go back and pick up the items that had zero on hand during the first pass and any new items that were created during the count cycle. Is there a way to create a count and add the new and now On Hand Quantity items to a count so I do not have