So I had replaced the heater core on my '99, after having done a coolant flush (a long one, using running water hose input to the radiator, and using the radiator drain plug, and running it until "clear", and then some. Probably ran the hose for a good hour. And yes, still some rust flakes in the otherwise "clear" water.
And, yes, after 1.5 years, the new core failed, sprung a leak. (That might have happened anyway, or might have been related to rust). I replaced the core again, a second time (went faster the second time but still a lot of work, and I also replaced the rear core that time even though it had not failed.) The front core failed a second time (with a different brand), and I used two supposedly reliable after market brands. The third cores are still going now. Radiator has been replaced once as well. Between the 2nd and 3rd front cores.
The back-flush is a good idea, though it is a hassle on the front core, because the quick disconnects are neither quick or easy, with 90 angle needle nose, or a make-shift special tool, or a real special tool. It is a hassle to get them to let go, and its a hassle to get them reliably put back on. (I had one hose blow off on a very hot day, in a very bad place, and nearly lost the engine - but didn't thanks probably only to running Mobil1 Synthetic oil which didn't burn. Engine dropped into crippled 4 + 4 alternating run mode (in order to do "air cooling"). Had to fix the dumb truck in a OReilly Parking lot 1/3 of the way on a 300 mi journy, after getting H20 at one place, and driving down the hill to get more coolant, and then doing the Grapevine I5 in CA a second time.).
Heater core flushes that is what most people do. Disconnect them once in a while. (I only do it about every 3 years, and then backflush (reverse direction) with a hose. Some people cut both the intake and heater core outtake lines, so that they can put in a "bypass" U and/or just straight through connectors that can be disconnected with easier access (compared to the quick disconnects on the heater core flanges themselves) to do these "yearly, or every2-3 years flushes.) Other people don't cut the lines, and mess with the disconnects.
If you ARE replacing the heater core, I recommend cutting the flanges off the old core, so that you can fashion your own "bypass" U that can hook onto the original quick disconnect ends of the heater core input output hose lines. And then just store that in the truck for heater core failure emergency. If the core is leaking or "steaming" inside it will fog up the inside with very hard to clean coolant "steam". So having a bypass U that you can install sooner on a trip will at least let you complete your trip (cold).
