Firstly, lovely mod. Wish I had it years ago.

As the title states, if you have a building flagged to swap modules or change quality, the blueprint shotgun will shoot at the building but the scheduled changes won't occur. What's more, it often wastes the items you're trying to apply. And sometimes, it duplicates the building in the same position such that when you try to manually delete it, you have to mine it multiple times for it to finally be removed.

If this behavior can't be reproduced normally, it be a conflict from either the Recursive Recycler mod or the Merging Chests mod ( https://mods.factorio.com/mod/WideChests ).