Dry the beef cubes with paper towels and then sprinkle them with salt and pepper to taste.
Turn on the Instant Pot and select "sauté' mode, adjust to more. When hot, add the bacon and cook, stirring occasionally until the bacon is lightly browned. Remove the bacon with a slotted spoon to a large plate.
In batches in single layers, sear the beef in the bacon fat for 3 to 5 minutes, turning to brown on all sides. Remove the seared beef cubes to the plate with the bacon and continue searing until all the beef is browned. Set aside. NOTE: you can also sear the bacon and beef over the stove in a skillet.
Add butter and when it's melted add carrots and onions and cook for 5 minutes, stirring occasionally, until the onions are lightly browned. Add garlic and cook for 1 more minute. Season with salt and pepper. Add Cognac, if using; cook for 1 minute.
Put the meat and bacon back into the pot with the juices. Add the bottle of wine and beef broth, tomato paste, thyme, and beef bouillon, if using. Mix to combine. Let it simmer for 8-10 minutes to evaporate the alcohol before closing the pot otherwise, the alcohol will not evaporate, and you will have the raw wine taste in your dish. Secure lid and close pressure-release valve.
Select Meat/Stew adjust to more (45min). When the time is over, let the pressure release on its own for 5 minutes. Then, carefully turn the valve to "Venting," to release any extra pressure that might still be in there. Then remove the lid. Press "cancel".
Mix flour and water until well combine and no lumps.
Select "sauté' mode, adjust to normal. Add the frozen pearl onions and the flour mixture. Simmer for 5 minutes, or until the onion are heated through and the sauce thickens.
Sprinkle with chopped parsley, if desired, and serve hot with mashed potatoes, rice, or polenta.