I'm sorry. You cannot now convert those files automatically, to take lines like
a = 5;
And automatically have MATLAB see those lines as
a = vpa(5);
with some number of digits specified, where all double precision numbers as created in all of your files are now converted automatically and on the fly to VPA.
Could you use some text processing to do so? That is possible if your code if pretty simplistic, but I would consider it suspect unless you are highly skilled at using tools like regular expressions in MATLAB, and even then, I'd be wary of bugs you may introduce.
Oh, and even if you could do this? Your code would now run quite slowly, because MATLAB is not optimized to use all symbolic computations.