Subject: Pardon my ignorance, but...
Author:
Posted on: 2012-02-23 18:02:00 UTC
Did you get Permission? If not, you shouldn't be writing PPC missions.
To answer your question, though, the standard rules of engagement apply: don't, if you can avoid it. The agents' SEP fields should protect them from notice by any canon character, including an A.I., providing they don't make themselves too obvious. In circumstances where the badfic makes the A.I.'s notice impossible to avoid, however, either the canon snapping back into place will remove the non-canon memories, or somebody from DoSAT can probably manually rewrite it.
When deciding how to handle a situation, the best answer is whatever is a) the funniest and/or b) the most growth- and development-inducing for your characters.
~Neshomeh