Soooo, my take....
I don't think shock cooling is really that big a thing...I mean, what happens when you fly through rain? Talk about quenching. I'm all for not tormenting your engine unnecessarily, but this was one of those things I wasn't particularly religious about. I'm sure more than one person has packed it in by doing an unreasonable amount of fussing with the engine trying to keep it warm and not really paying attention to the flight path.
Ok, that said, on the flip side, you can really smoke a big bore Conti fairly easily, so the real focus should be on the mixture. As long as you got to the cowl flaps eventually, you aren't going to do any "ooops...<bang>" damage. Trying to go around, getting back into the pattern or busy joining the missed approach while you're at a lean mixture while WOT? Yea, that will be far, far worse than leaving the cowl flaps closed for a little bit.
My personal technique was to open them entering the pattern, or once my primary descent to IFR vectoring altitude was done, for the reasons stated above. You're going to be slowing up, and may be operating at more than idle, especially if vectors are extensive or the pattern is widebody style. Open them when the workload is low, so you aren't missing them when it is high.
CHT is key to cylinder longevity. The key to managing the CHT is know what your EGT/TIT should be and how to manage it. The yield curve isn't linear, and once you get above 420, you start eating into cylinder life. I personally set my JPI to alarm at 390. It wasn't "OMG 390!!!! master warning!", but a reminder to take steps to stop the increase. Crack open the cowl flaps, lower the nose, richen/lean the mixture depending on which side of peak you were on, etc.
I had a 550 with the TAT turbo in my V35. It was PACKED in there. I ran it LOP, but ran it by the TAT book and had the fuel controller dialed in. My CHTs never got above the low 300s in the climb and the TIT was in the low 1200s (well, ya, burning 35 GPH, you were practically drowning it). Once in cruise, running at WOT/2500 with 17.5 GPH, that was about 80d LOP, and my TIT was around 1440-1500. CHTs were in the mid 300s, and I had one outlier that would float around 380 if the weather was really hot. For descents, I'd pull it back to 18-21" and stick the nose over, and I got what I got. Bottom of the descent, level off, power up to 25", open the cowl flaps, and you were done fussing. The big, big, big takeaway with the TAT was you absolutely HAD to get the mixture rich for a go-around, otherwise the temps would get hot in an instant.
FWIW, you need someone who knows WTF they're doing if you're tinkering with the fuel controller. They need to follow the Continental SB TO. THE. LETTER.