There are many areas of the AXL schema that involve lists or collections of items that belong to other items. In some (possibly most) cases, AXL exposes only the ability to update the collection as a whole. For some of the more common/popular requests where this is particularly painful, the 'addXXX/removeXX' mechanism is provided.
Essentially providng this for updateRemoteDestinationProfile/lines (and possibly many other similar collections) would be an enhancement request.
If this limitation is particularly difficult to work with, you may be able to accomplish the same thing via custom SQL queries and executeSqlUpdate, though that will carry its own set of caveats.