Show us the loop code for context...
Is the condition that there is only one variable in the files that are not to be sorted (by inference from the ==1 above)?
If you're reading the files into a table and the above is the case, then simply
for i=1:nFiles % loop over all files from a dir() or however determine
t=readtable(file(i), ...); % read each in turn
if width(t)>1 % check on number variables,
t=sortrows(t,...); % >1, sort
end
... % do whatever else...
end
