I understand that you want to perform two tasks. First, you want to combine the data from 5000 text files into a single text file, perform some operations and then split the text file into new output files.
For both the tasks, you can use fprintf() function. Remember to open and close files using fopen() and fclose() . When using fopen() on a file that is not present in the path, MATLAB will create a new file.
A = [1 2; 3 4];
fid = fopen('file.txt','w');
fprintf(fid,'%d %d \n',A);
fclose(fid);
If you want to override textfiles you may use writematrix() function.
