Melt 1 tbsp butter in the cooker. Add the bacon and fry until crisp, stirring occasionally, about 4 minutes. Use a slotted spoon to transfer the bacon to a bowl.
Add half the short ribs and brown them well on all sides, turning occasionally, about 10 minutes. Transfer these to that bowl and add the remaining short ribs, browning them in just the same way. Transfer these to the bowl, too.
Add the onion and cook, stirring often, until softened, about 3 minutes. Add the mushrooms and continue cooking, stirring occasionally, until they give off their internal moisture and that liquid evaporates to a glaze in the pot, about 5 minutes.
Pour in the wine and deglaze the bottom of the inner pot. Turn off the sauté function and stir in the stock, thyme, sage, salt, pepper, and bay leaves. Return the short ribs, bacon, and any juices in that bowl to the pot. Stir well, then lock the lid onto the cooker.
Press Pressure cook for 1 hour and 30 minutes followed by natural pressure release.
Once the lid has unlocked, open the cooker and find and discard the bay leaves. Use kitchen tongs and a slotted spoon to transfer the short ribs, bacon, and any vegetables to a serving platter, and cover to keep warm.
Use a flatware tablespoon to skim any excess surface fat from the sauce in the pot, then press Sauté, set time for 5 minutes.
As the sauce comes to a simmer, use a fork to make a smooth paste out of the flour and the remaining, room-temperature 1 1/2 tbsps butter in a small bowl. As the sauce simmers, whisk this flour mixture into the pot a little at a time, whisking until it’s all been added and the sauce has thickened, 1 to 2 minutes. Turn off the Saute function and pour the sauce over the meat and vegetables on the platter.