This is a known issue with some Themes. It occurs if the cart page has non-standard line item quantity inputs in your theme. The app can not properly get the line item quantities, so the line item is removed from the cart.
The app relies on the fact that all the quantity inputs have id attribute with line item variant id inside.
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Usually the id attribute looks like "updates_742384782", where 742384782 is Shopify variant ID.
There are 2 possible cases:
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