Any building capable of placing on either lane of a belt which is facing away, like inserters, mining drills, and recyclers, don't preserve their flip if you upgrade them with the upgrade planner, and then blueprint shotgun to place them. Instead, it reverts to the unflipped state. I have confirmed this is an issue with Blueprint Shotgun because I tried having bots place them, and they place the buildings correctly.

It's worth noting that I'm playing with Quick Adjustable Inserters, but I don't think the mod would affect mining drills.

The behavior might be related to fast replace. Fast replace, on my version, also reverts to the unflipped version. And that's a vanilla feature.

Thanks for the report, fixed in 0.3.4