Whenever I have an existing product, that has operations already (inventory movements, sales, etc) and create a new variant on it, all inventory history is erased from the existing product.
If I have a white t-shirt as a product with no variants, and then I create a Red color variant, all history in the white color t-shirt is erased.
Inventory History Guardian saves your product variant’s history for each location and saves them beyond Shopify’s 90 day limit and is not affected by variants being added or removed.