I found the solution thanks to a reddit user.
File2 = stlwrite(TR, 'file2.stl');
This line is wrong. Even if the library says the order is fine, it is not. It should be:
File2 = stlwrite('file2.stl', TR);
Now, to prove it yo can do the following:
[F, V, N] = stlread('FileBefore.stl'); % Notice that this line had a variable name File1 previously.
% That was wrong. stlread is a command like plot() and you can use
% it alone or with [F, V, N] to get those values.
stlwrite('FileAfter.stl',F,V); % You can just write the same file under another name to see that
% it works. If you gave stlread a variable name (File2 for example)
% you can use it here too.
% Now if you change V by multiplying it by 2, it should work just fine