I assume you're asking was there a flag that didn't have stars representing the Confederate States? In that case, no, not officially. Even when West Virginia broke away from Virginia, the official flag gained a 35th star (which still included Virginia and all the other rebelling states). In the view of the US, you can't actually secede from the Union (there was a Supreme Court Case affirming this). They viewed the Confederacy as a group of rebelling states rather than an actual nation. Creating a flag without those states could be seen as official acknowledgment that they were in fact their own country, which as you said, would be a little counter-intuitive on their part.

There were unofficial flags made called "exclusionary flags" that only had stars for the states that were still in the Union. Generally the number was in the mid-to-low 20s. This was carried over from an earlier abolitionist practice of making flags which only had stars for free states. The same technique was later used by suffragists and proponents of marriage equality.

Officially there was no distinct flag for the North, and the government discouraged people from removing stars for the reasons captmonkey has said.