That depends on whether you counted the bin location at all. If you count a bin location, it is considered fully counted: products that Pickware lists there but that you don't record are saved with 0 and booked to a stock of 0 when you finish. Bin locations and products that you don't count in the stocktake at all, on the other hand, remain unchanged. Pickware does not set them to 0 automatically.
On a counted bin location
When you save a count for a bin location, Pickware includes all products with stock on that bin location in the count. Anything you haven't recorded then appears with the amount 0 in the Counted tab. This applies to counting per bin location in the WMS App just as it does in the Shopware Admin. In the Admin, you therefore only save a bin location count if all rows of that bin location are checked.
A stock of 0 is correct if the product is actually no longer on the bin location. It becomes wrong if you only partially counted a bin location or overlooked a product. As long as the stocktake isn't finished, you can correct this in the Counted tab, see Correct stocktake counts and add products afterwards.
Attention: This also applies to inactive products and to products that you have hidden using a filter. When saving, Pickware sets everything that has stock on the bin location to 0, regardless of what was visible in the list.
On bin locations you don't count
If you don't count a bin location in the stocktake at all, its stock stays as it is when you finish. When you click Finish stocktake, Pickware notifies you that the stock of uncounted products is neither adjusted nor set to 0. This way, you can also count only part of your warehouse, such as a single shelf row.
If you want to deliberately set uncounted stock to 0 because the goods are no longer there, enter a 0 in the Counted column in the Uncounted tab. Then select the rows and click Apply all selected counts. For a single bin location, you can also do this via the row's context menu with Save stock count.
What applies to products without a fixed bin location?
Products without a fixed bin location are stored on the Unknown bin location. The rule for counted bin locations does not apply there: if you count a product on Unknown, the other products there are not automatically included with 0. Uncounted stock on Unknown remains in place. Multiple counts of the same product on Unknown are added together instead of overwriting each other.
You can find the complete process in Performing a stocktake: process from start to finish.