What happened to the art in "Our Father who art in Heaven"? And why is it art, and not is?
Art was the second person singular form of the verb "to be" in older versions of English. Over the centuries, it eventually became are (along with the disappearance of the -st suffix across all 2nd person singular verb forms). Is, on the other hand, would be the 3rd person singular form.
The reason are is used instead of is is because the prayer is speaking directly to "Our Father": i.e. "You, who are in Heaven".
It's also worth nothing that art is the second person informal. Because it sounds archaic and harks back to an era of more explicitly marked respect, this form is often mistaken for the formal. It may also surprise some that God is addressed informally, but this is true of other languages as well (cf. Spanish "Padre nuestro que estás en los cielos").
As far as what happened to it (i.e., why some churches use it and some do not) the Lord's Prayer is generally considered to be Matthew 6:9–13 (Luke has a differing version). As it is a Biblical excerpt, as churches adopt new translations as canon the canonical Lord's Prayer for that church changes.