If you keep everything tables, you can use the VariableNames property to indicate which variables are being updated. MATLAB is able to align the variables by their names. See more on how ot access data in tables here.
% Create a table with 4 variables
SQ1 = (1:5)';
SQ2 = SQ1;
SQ3 = SQ1;
SQ4 = SQ1;
A = table(SQ1,SQ2,SQ3,SQ4)
% Create table B from 2 variables from table A
B = A(:,["SQ2","SQ4"]);
% Modify B
B_corrected = flipud(B)
% Use the variable names of B_corrected to replace the values in A
A(:,B_corrected.Properties.VariableNames)=B_corrected