I rather hope this will get fixed when we make depth not be a thing, but:

• incremental /sync looks for rooms you have joined since your previous sync
• it does this by looking at your membership state in each room at your 'since' token (

  synapse/synapse/handlers/sync.py

  Line 1087 in 933bf2d

  old_state_ids = yield self.get_state_at(room_id, since_token)

  ish), and looking for those that are not 'join'
• however, get_state_at uses get_recent_events_for_room which returns the event with the greatest depth, so if somebody has been playing silly buggers with the depth, you may end up looking at a point in the graph where you were a member, even though at the point of the 'since' token you were not.