The Communication Center supports a "priority" system that essentially makes two messages work as counterparts to one another.  If two messages are set to go out at the exact same time (exact same Message Trigger filters), and a customer's order could qualify for both messages at once, then by default the Communication Center can cancel the two templates out as it does not want to potentially spam your customer. This happens only if orders could potentially qualify to receive both templates at once (if, for example, they are both non-product specific templates). However, this is not the case if the two templates are meant to go out to separate sets of SKUs and/or ASINs.
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To make this work, you must ensure that both messages are set up with the exact same Message Trigger parameters, including any configured Advanced Filters. The only difference between the counterpart templates should be that one template has a corresponding ASIN or SKU specified in the Item Filters, and the other template has no ASINs or SKUs specified.  The Communication Center will then "prioritize" the template with ASINs/SKUs specified over the non-product specific template. 

We've provided examples of a General Message and a Product Specific Message below:
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​ (1) Example General Message

​(2) Example Product Specific Message