...
There are 2 possible cases:
1. line item quantity input in your theme doesn't have the id attribute at all or this attribute doesn't contain variant ID value.
Example: {{id="updates_{{ line_item.id }}"}}.
2. line item quantity input in your theme contains variant ID inside the id attribute, but it has another prefix (not "updates_").
In the case (1) you need to modify/add the id attribute to make it look like "
...
...
id="updates_{{line_item.id }}
...
" ". Just use corresponding liquid variable in the cart.liquid.

(click to enlarge)
...