"That is" vs. "i.e."

I use them interchangeably. kiamlaluno sees a distinction I'm not aware of; even in the specific examples he cites, I would use them interchangeably.

The actual term i.e. is an abbreviation of id est in Latin, which literally means "that is". In fact, when I see i.e., I cannot help but say "that is" in my head; this helps me distinguish it from e.g. (exempli gratia, by the way).

If the editor had it changed, it was probably because "that is" is a little clearer, perhaps to non-primarily English speakers.

That is is used to introduce or follow a clarification, interpretation, or correction of something already said; i.e. is used to add explanatory information or to state something in different words.
The difference is that i.e. doesn't follow a clarification; it is not used for corrections, too.

Those walking boots are synthetic, i.e., not leather or suede.
He was a long-haired kid with freckles. Last time I saw him, that is.
Those are androcentric—that is to say, male-dominated—concepts.

In the second example, you don't write "Last time I saw him, i.e."

The editor most likely changed i.e. to "that is" because according to the APA you should replace all instances of i.e. to "that is" in the body of the work. It states that i.e. should only be used in parenthetical material. I am not so familiar with other style types (if the journal uses something other than APA) - but I edit papers for journals and I always replace i.e. with "that is."

"i.e." is the Latin abbreviation for "id est" and is often used in place of the English translation "that is". However, in formal written English it is more appropriate not to use abbreviations. The same applies for the use of "for example" rather than "e.g.".