The idea is that you run the regexpr N times using the 'once' parameter. And you don't need so save the file intermediately after you have converted all the numbers to 0.
function changeTC_SYS(filename, N)
content = fileread(filename);
content = regexprep(content, '(?<=set TC_SYS_\d*\s+)[01]','0');
for i = 1:N
content = regexprep(content, '(?<=set TC_SYS_\d*\s+)0', '1', 'once');
end
fid = fopen(filename,'w');
fwrite(fid,content);
fclose(fid);
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