This is the second-most asked question. It's one of the most common questions we get. It's so common, there's a post about it on the Arbortext Code Archive.
On save, Arbortext Editor adds processing instructions, like <?Pub Caret?>. How do I remove processing instructions (PIs) ?
Turning off the PIs is easy. You change an advanced setting in the preferences:
It's documented in help topic #1587.
If you turn off the PIs, you turn them all off. No touchup, no Arbortext extensions, etc. Make sure you really want them off before you turn them all off.