If I have Comfey in play and I use its "Flower Selecting" Ability, can I then use Thorton to switch it with a different Comfey and use "Flower Selecting" from the new Comfey?
No, that won't work. Even though the new Comfey is a different Pokemon than the first one, it remembers the Flower Selecting Ability was already used this turn so you cannot use it again on that Pokemon.
Source: TPCi Rules Team (2022-09-29)

Relevant cards

Note: All applicable cards may not be listed below.
SWSH11_167
SWSH11_167
SWSH11_79
SWSH11_79