Hi ,
Unfortunately, there isn't a way to detach painted or scattered vegetation from the surface it has been applied to, so making large changes to the mesh and then re-importing would cause the vegetation to disappear.
There are long term plans for a very significant overhaul of the foliage system, and ideally limitations such as these could be overcome, but for now there isn't a good workaround for avoiding this behavior.
If you have any ideas you think would be useful to add to Twinmotion, please submit them on our roadmap here and the developers can take it into consideration for future updates.
Best,
Raghib