Wolfram Language, 117 bytes

StringReplace[RegularExpression["\\b[[:alpha:]]{2,}\\b"]:>StringDrop[StringInsert["$0",StringTake["$0",{-1}],-3],-1]]

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Applied to the test strings.

StringReplace[
  RegularExpression["\\b[[:alpha:]]{2,}\\b"] :> 
   StringDrop[StringInsert["$0", StringTake["$0", {-1}], -3], -1]] /@
 {"Thansk", "Youer welcoem", "This is an apple", 
  "Flippign Lettesr Aroudn", "tHe oDd chALlEneg wiht swappde lettesR"} // Column

Thanks

Youre welcome
Thsi si na appel
Flipping Letters Around
teH odD chALlEnge with swapped letteRs