GlennW1173, I've read through your post several times. I have a similar situation with my 2015 Passat TDI SEL Premium. Only mine did not overheat, but the coolant temperature gauge in the instrument cluster went beyond it's normally stable 190 deg F yesterday. I did some diagnostics and reading, and I'm pretty certain my problem is with the switchable coolant pump in the main (large) high-temperature circuit. There is a lot on the intranet with this pump not retracting a shroud properly. An extended shroud covers the impeller to prevent coolant flow through the block & radiator (used to warm up the block quicker). The shroud retracts when a solenoid releases and a spring moves it to a retracted position. Seems like something goes wrong with the spring retraction over time, causing the pump to not circulate coolant. In my case, the coolant temperature gauge in the instrument cluster got up to an estimated 235 def F as I was pulling into my garage. I left the engine running and opened the hood and felt both the upper & lower radiator hoses - both were cold, but both radiator fans were running full speed. In looking through the 3 cooling circuits on a 2015 Passat EA288 engine, the switchable coolant pump is the only pump of the 3 used in these circuits that could cause an engine coolant block temperature to go above normal (along with a thermostat frozen in the shut position).
The secondary coolant pump you are having replaced (Part No. 2Q0-965-587-A ) is called a V488 Heater Support Pump in my EA288 Engine Management booklet. This pump is used in the circuit that supplies coolant to the heater core and to the EGR cooler. It is a pump that pulls hot coolant from the engine block through the EGR cooler and the heater, returning the somewhat cooler coolant back into the engine block. If it failed, it would not cause an engine to overheat (would not cause your instrument cluster coolant temperature gauge to go beyond a normal 190 deg F reading). At least this is what my findings are telling me. I would share with you the section of my EA288 Engine Management Booklet focused on the cooling systems on the EA288 with you, but it is a PDF file and apparently can't be attached to posts in this forum.
Also, per this part of your post: "From what I understand the secondary coolant pump is critical to cool the engine after the TDI regen process is complete. The lack of proper cooling is what likely blew the cooling system components on 8/15 and 8/19. My understanding also is that the regen cooling system is now under more stress because of the TDI reprogramming." This isn't quite correct. The secondary coolant pump is critical to cool the EGR during the TDI regen process, because the exhaust gas recirculation temperatures are elevated quite a bit during a regen process. On EA189 diesel engines, the EGR was under significantly more stress during the regen process and has cause many problems on those engines. The EA288 diesel engine, which you have, really did not change as this engine was much closer to actually achieving its emission limits before the dieselgate fixes were implemented. My regen cycles were unchanged after the emissions fixes, and exhaust gas temperatures reached during regen cycles were also unchanged. So in this respect, the EA288 engine is little if any affected by the emission fixes implemented.
I'm hoping your Denver VW dealer got it right though. If not, the switchable coolant pump replacement will be an expensive repair as this pump is driven by the timing belt, meaning a lot of stuff has to be removed and the engine supported (because an engine mount has to be removed) to access this coolant pump. Might as well do a full timing belt replacement with idlers and all then too. I would be very careful your first few miles and would be watching that temperature gauge. I guess you will know more tomorrow.
I will keep a eye on mine. 111k miles so far and all good. She’s deleted as well.
