Can you please provide the exact setup you have encountered this issue? I have just tried replicating by:
1) Create a Behaviour Tree Owner with a bound graph.
2) Create a SubTree node in that bound graph.
3) Clicked the “circle” icon in the SubTree node, to assign an asset Behaviour Tree through a blackboard variable rather than directly.
4) Finally, I override some of the exposed variables of that asset Behaviour Tree and enter play mode (with Domain Reload enabled).
Is that a correct reproduction for the issue you are facing please?
The overriden values are all still there in my test above. Please note though, that if you change the assigned SubTree (eg the blackboard variable that holds that SubTree change), then the variables mapping values will indeed reset since only one subgraph variables mapping table is serialized (at least at the moment).