I thought I'd come back and update this post as I ended up having the transmission serviced.
I found an independant transmission shop to do the work and he had done lots of fords that use the same zf 6 speed transmission. Cost was $688AU to change the fluid, pan and filter, 4 round tubes seals, square/rectangular seal and the plug seal. The fluid was very dirty and the seals were going hard and pressed flat so they needed to be done.

It does drive much better and the 2-1 bump is gone when cold. Once warmed up it still does have the 2-1 bump but it is a lot less pronounced. It pretty bad before the service and it is noticlably better now but it will still be present if i roll very slowly to a stop.

Couple of options I have now are
1. Do the software update myself (although I'm not keen on this option as i don't have the voltage stabilizer and don't want to risk bricking it)
2. The transmission shop suggested calling BMW and see what they will charge to update the software modules, he said it should take more than an hour so probably be around $220AU.
3. xHP Flashtool - I've been reading up on this and it could be an option. This looks like it remaps the transmission with some improvements. I don't know if this would cure the 2-1 bump though...

I ask about resetting the adaptations, he didn't recommend doing it. He said it will adapt was i drive it around. Any thoughts on this and is it worth doing?

I’m using XHP on my E70 6hp28.
Tried stage 2 & 3. It flashes fast .
On my e53 6hp26 I used to have the bump and just serviced it myself and it went away . I agree about not resetting adaptions . Everyone does it , so it’s easy to do with ISTA if you want;
but it adapts to wear of the clutches etc. so my thinking is you want the transmission to be adapted to current level of wear.

What fluid did the transmission shop use?

The fluid and pan/filter were geniune ZF. The rubber seals and plug adapter were aftermarket. He said he has been using the aftermarket seals and adapters for a long time without issue.

When you serviced the e53 6hp26 did the 2-1 bump issue go away straight away or did it take some time? I was wondering if the transmission will take a bit of driving to adapter to the new fluid and seals?

With XHP does it just download the software straight from your phone to the car? I have plugged it in and got it to read the my transmission and that all worked fine. It made a backup of my transmission then was able to see some wear values.

I actually serviced it twice to try and get a greater percentage of new fluid in there. I didn’t use genuine Lifeguard fluid as I’ve got a XR6 turbo with a ZF 6hp26 and used other fluids in that so knew it’d fine, I think the bump was gone pretty much immediately.
With XHP I wasn’t able to use my phone;
I used the same cable I use with NCS/ ISTA/ etc and a windows laptop.
I don’t know if XHP will fix your bump. I think you can see current adaptions in XHP but not reset them , as XHP doesn’t recommend it.
I flashed it without even a battery charger connected.

https://xoutpost.com/attachments/x5-...c-software.pdf
I done that update just turn off all acc like stero ecta and updae took like 20 mins using NCSEXPER and D can cable for my E53 N62 with 6HP i done the seals ecta and used all ZF parts and fuilds with mine with the relearn is not simple as reset and fix it self there is produre that follow afte it like takes 1 hr for it .

That sound like the fix I need but i note it only references 4.4 and 4.8 models. Mine is a 3.0 diesel engine, model year is 2005.
I thought updates for transmission modules were done through winKFP?

I followed this you need liek chrome to change it english https://m.blog.naver.com/livinda/220790197476
All can say is check the GS19 Version on yours and see if maches the version update .

did they install the Sonnax Zip Kit?

No they didn't any kits. Just changed the seals, plug adapter and fluid.

How do you find xhp? It looks like a good product and the option to have the gear display on the cluster looks pretty neat. I thought i might be able to use it to sort the 2-1 bump as i see it enables you to change shift parameters. Mine only has the bump in D mode. In S mode the bump isn't there so my thinking is the car shifts down to 1 while you are travelling faster and it isn't noticable in S mode. By the time it stops in S mode it has always changed to 1 so there is no bump. In D mode I can slow gently to a stop and will always get the bump. If i stop quickly the bump still happens, it just occurs with the car stationary and you have your foot on the brake. The only time i might not get a bump in D mode is when the car is cold, once it warms up it will be there.