Sorry my earlier response wasn't very well-crafted. I'll try to make it a little more clear, though I fear you won't much like the answer.
The way the mod works is that once you enable stock by attribute it takes over the management of stock levels for all products with attributes. So if you have a product with attributes for which you do not create any variants and give them stock, then when a customer tries to buy them, the mod will return zero stock levels. This is not immediately obvious as the product stock level is not updated when the mod is first installed, but when you sync the stock, the product stock will go to zero. Products that have no attributes will continue to use the product stock level.
You can return to using only product level stock figures by uninstalling the mod (basically by over-writing the six core Zen Cart files changed by this mode and listed in the release notes with the equivalents from a default Zen Cart installation. You would then need to reset the stock for those products to which you had allocated product variants or synced the stock values.
Can you tell me a little more background to what you are trying to do so that I can take it into account for future Attribute Stock requirements?
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