Makes no difference. Ford did an excellent job in the programming for the EEC-IV computer, better than most manuals give them credit for, and it adapts very quickly. Personally, if I do something it'd better be drastic before I reset the computer. Even then, I just go directly to beating the snot out of it (after warming up) to ensure the computer knows exactly what its job is going to be like.
I've never had a problem, and I think if people do have problems it has more to do with the mods in relation to the computer accepting them as normal inputs, crunching the numbers, and adapting to them. Sometimes it's the adaptation that makes people go nuts, too. Planning ahead goes a long way.