TA's have always had the ability to amend bookings via the GDS platform so I cannot see any reason why they also cannot leave a booking open.
I've made changes to airline bookings (upgraded etc) in the past via a travel agent without any issues.
It's the other way around as well in that VS actually have very limited change capacity when it comes to GDS (travel agent) bookings. This is why if you book via a travel agent and try to contact the airline directly to make a change, they won't be able to do anything and will tell you to contact the travel agent.
Any flight schedule changes will get updated from airline but that's all.
All airlines use 2 platforms when it comes to booking airline tickets. There's the GDS (global distribution system) platform. See
WiKi for more details. This is the platform travel agents use to use to book tickets (this includes all online flight resellers).
There's then also a direct booking platform which is the system the airline uses for their own online and call centre made bookings.
Whilst a booking made via the GDS system 'mirrors' on the airlines main reservation system (hence why you see TA flight bookings in exactly the same way on airline website view bookings), those bookings are locked to the travel agent who originally booked it and so an airline reservation agent won't be able to do anything other than view it.