As detailed in this article, the floods probably explain some of the huge swings like Breathitt and flips like Letcher.
But they can't explain everything. Hal Rogers' district, which includes Eastern and South Central Kentucky, is one of the most Republican and Trumpian in the country, and Beshear outperformed Biden there by a whopping 45 points. The Beshear brand is apparently still strong in the Eastern region of the state, with some ancestral Dems still seeing a distinction between the state party and the national Democratic Party. Way more than I thought, actually.
Honestly, I think there's mounting evidence Appalachia peaked for R's in 2016. It's not going to vote Dem under normal circumstances anytime soon, but I do think these voters expected something fundamentally different from Trump-era R's on economics than they got, and they clearly aren't as pro-life as assumed. It's starting to show, particularly in oddly-timed elections when they have to be motivated to turn out. D's didn't win anything of note, but they did do oddly well in the contested western VA races compared to the statewide results.
I believe it's just turnout differentials (79% of Biden voters turned out in KY versus 52% Trump voters. Turnout in MS also favored Ds but less so). I have to see the Appalachia trend significant blue in a Presidential election to believe it.