These are all sort of special cases.
Warsaw had a hostile host hotel owner as previously mentioned.
The original Joplin supercharger was put at a hotel undergoing renovations. It was a construction site for years and then eventually they stopped working on it. No idea what happened, but somehow the renovation plans fell through. It gets my vote for worst ever supercharger location as there was even a lot of tire-piercing debris in the supercharger area due to the construction site. It made sense to shut it down when they opened the new one a couple miles away.
Beaver got a major upgrade, first adding stalls and then adding a ton of v3 stalls. Once there were 24 v3 stalls, the original 4 v2 stalls were mostly irrelevant anyway. It is also undergoing some construction. The car wash in the middle of it is being replaced with a coffee shop so maybe they wanted some non-Tesla parking available for their employees and customers. If you had to give up a few stalls, it makes sense that the old v2 stalls would be the first to go.
But yeah, none of these were direct upgrades per se. All of them had new stalls or location built, and then gradually phased out the old stalls/location. There was a time when both v2 and v3 were operating simultaneously in all cases.
Kettleman City is the one example I can think of where stalls were actually upgraded, but I also consider this a bit of a special case since it is a rare supercharger location where Tesla owns the entire property. I think it was done partly as a v3 prototype and partly to help with a busy Tesla corridor.