If you try to do this manually, there's no way to get the second one to not become an input to match the other output. I understand why this works the way it does, but I'd like to have a way to opt out of that behavior. (this part is just a feature request)
Separately, and why I'm reporting this as a bug...
If you place a blueprint with an underground belt that happens to match another nearby belt, the type (input/output) of the underground belt entity can get silently flipped. I do not expect that this is often, if ever, the desired behavior. This can happen with completely legitimate blueprints.
Worse, if you have a blueprint that explicitly includes mismatched underground belts, one of them will get flipped. It appears correct in the blueprint edit window, but the cursor ghost has one of them flipped, and the entity ghosts get place flipped.
Here are two example blueprints that exhibit this behavior:
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0eNqVkN0KgzAMhd/lXHfgxAn2VcYQf4IEtJWaDqX03efPGGNjF7tJQsL5cpKAuvc0OjYCHUBGWJgm6GtAy44aYWugM3WMltL4oSYHfVYw1UDQ8KYl1zm75lNNvUBhtBMfwoAZOlFY1hgVZBk3ifUyekFU4ROb/o09pd/cmwI31hxn8Aqad8MTd6bqN/XvHU8SCw2IO2ir9NubFO7kpt1GnmXpJSmKNM/iq13Wi2yIBPEB9251cA==
PS: I also think it's a bug that deleting an input can cause an output to flip to an input if there's another output for it to pair up with.
PPS: To create the second blueprint: create a north underground input A, matching north underground output B north of A. delete A. create a south underground input C south of B, matching south underground output D. Drag a blueprint across all three entities, then in the blueprint editor right click the middle entity to clear it. Save or export the blueprint.