Tristaan, good question.

Here's my advice.

What Not To Do

Be careful not to imply to the auditors that automated tests are as effective as manual tests in cases where they are not designed to cover as much as the manual tests would. Julian Harty made this point eloquently in one of his recent presentations. I've included two of his slides below. His full presentation (which is quite good) is available here.

What To Do

Keep a clear record of what the automated tests actually test (and what manual tests are designed to find that the automated tests could well miss.

Tristaan, good question.

Here's my advice.

What Not To Do

Be careful not to imply to the auditors that automated tests are as effective as manual tests in cases where they are not designed to cover as much as the manual tests would. Julian Harty made this point eloquently in one of his recent presentations. I've included two of his slides below. His full presentation (which is quite good) is available here.

What To Do

In addition to the other good advice in the other answers, keep a clear record of what the automated tests actually test and do not test (as well as what manual tests are designed to find that the automated tests could well miss).