OK so @riking was right.
Just a little more detail and we are there.
Note I have already updated the wiki here -
selectively mark notifications read
POST Body - topic_id=1234&topic_time=1234&timings[X]=1234
Where X = post_number to mark read
note: this accepts multiple posts (based on comment a user is viewing) eg.
curl -X POST -d topic_id=1234 -d topic_time=1234 -d timings=1234 -d timings=1234 -d timings=1234 http://localhost:3000 /topics/timings.json?api_key=test_d7fd0429940&api_username=test_user
will mark comments 1, 2 and 3 read on the topic 1234