ClearAll[f1, f2, f3]
f1 = Module[{l = #, i = Position[#, _, {-1}, Heads -> False]},
ReplacePart[l, Thread[RandomSample[i] -> Extract[l, i]]]] &;
and a modification of Ray Koopman's copyPartition
f2 = Module[{i = 1, l = RandomSample @ Flatten @ #}, Map[l[[i++]] &, #, {-1}]] &;
Examples:
lst = {{"Q", "W", "E", "R", "T", "Y", "U", "I", "O", "P"}, {"A", "S",
"D", "F", "G", "H", "J", "K", "L"}, {"Z", "X", "C", "V", "B", "N", "M"}};
lst2 = {{"Q", "W", "E", "R", {"T", "Y", "U", "I"}, "O", "P"},
{"A", "S", "D", "F", {"G", {"H", "J"}}, "K", "L"},
{"Z", "X", "C", "V", "B", "N", "M"}};
f1 @ lst
{{"C", "H", "X", "I", "P", "Q", "O", "V", "D", "U"},
{"S", "E", "L",
"R", "A", "F", "W", "T", "K"},
{"Z", "G", "J", "Y", "B", "M", "N"}}
f2 @ lst
{{"U", "A", "D", "Z", "E", "R", "N", "L", "S", "O"},
{"X", "V", "J",
"B", "H", "P", "I", "K", "T"},
{"M", "C", "F", "G", "Q", "W", "Y"}}
f1 @ lst2
{{"O", "B", "P", "D", {"E", "A", "J", "Q"}, "I", "H"},
{"T", "R", "Y",
"C", {"N", {"L", "S"}}, "U", "W"},
{"V", "Z", "K", "M", "G", "X",
"F"}}
f2 @ lst2
{"F", "J", "K", "Y", {"Z", "D", "W", "A"}, "P", "R"},
{"L", "T", "G",
"H", {"I", {"U", "S"}}, "V", "E"},
{"N", "C", "B", "Q", "O", "M",
"X"}}
Table[f1[lst], {3}] // Grid // TeXForm
$\small\begin{array}{ccc}
\{\text{Q},\text{Z},\text{P},\text{B},\text{J},\text{U},\text{I},\text{S},\text{E},\text{M}\} &
\{\text{T},\text{H},\text{F},\text{D},\text{W},\text{Y},\text{K},\text{O},\text{R}\} &
\{\text{X},\text{C},\text{V},\text{G},\text{L},\text{A},\text{N}\} \\
\{\text{Q},\text{S},\text{I},\text{V},\text{T},\text{R},\text{Z},\text{X},\text{N},\text{F}\} &
\{\text{U},\text{H},\text{E},\text{B},\text{G},\text{W},\text{O},\text{K},\text{C}\} &
\{\text{Y},\text{D},\text{M},\text{A},\text{P},\text{L},\text{J}\} \\
\{\text{X},\text{V},\text{B},\text{M},\text{L},\text{K},\text{F},\text{H},\text{E},\text{T}\} &
\{\text{I},\text{R},\text{U},\text{O},\text{N},\text{Q},\text{S},\text{C},\text{J}\} &
\{\text{A},\text{Z},\text{G},\text{Y},\text{D},\text{P},\text{W}\} \\
\end{array}$
Table[f1[lst2], {3}] // Grid // TeXForm
$\small\begin{array}{ccc}
\{\text{Y},\text{Q},\text{J},\text{P},\{\text{W},\text{T},\text{I},\text{L}\},\text{K},\text{O}\} &
\{\text{G},\text{A},\text{S},\text{N},\{\text{M},\{\text{C},\text{H}\}\},\text{F},\text{V}\} &
\{\text{D},\text{B},\text{R},\text{Z},\text{U},\text{X},\text{E}\} \\
\{\text{A},\text{E},\text{L},\text{M},\{\text{H},\text{T},\text{U},\text{Z}\},\text{F},\text{I}\} &
\{\text{N},\text{D},\text{X},\text{O},\{\text{S},\{\text{B},\text{J}\}\},\text{V},\text{C}\} &
\{\text{G},\text{Y},\text{W},\text{R},\text{P},\text{K},\text{Q}\} \\
\{\text{H},\text{T},\text{N},\text{A},\{\text{E},\text{G},\text{K},\text{U}\},\text{B},\text{P}\} &
\{\text{Y},\text{V},\text{W},\text{L},\{\text{D},\{\text{S},\text{Z}\}\},\text{F},\text{X}\} &
\{\text{Q},\text{R},\text{J},\text{M},\text{O},\text{C},\text{I}\} \\
\end{array}$