Drain clam juice from 2 cans into a 2-cup liquid measure and fill with water to the 2-cup mark; set aside. Drain and discard clam juice from the remaining can.

Turn on the Instant Pot and select the Sauté function. Add bacon and stir occasionally until fat renders and bacon is cooked, but not crispy, about 5 minutes. Add onion and butter. Cook and scrape the bottom until onion softens, about 5 minutes. Cancel function.

Add potatoes and clam juice-water mixture; stir. Close and lock the lid and set high pressure for 4 minutes. Allow for pressure buildup (10-15 minutes).

Allow to rest for 3 minutes, then release pressure carefully using the quick-release method (about 5 minutes). Unlock and remove lid.

Mash potatoes to desired consistency. Select Soup function, and stir in flour, thyme, garlic powder, salt, and pepper. Add evaporated milk and drained clams.