Thank you for the additional clarity!
You would need to setup something to copy over the data from the old BP component to the c++ component due to the engine seeing it as a new component.
An example would be to copy the data of the old BP component on PostLoad of the new c++ component and once it’s copied you’d delete the extra BP component.
There is also this function; UEngine::CopyPropertiesForUnrelatedObjects that you can use to attempt to copy as many properties as possible from the old object to the new one.
For your convenience here’s some references for scripting related discussions
Deleting Subobject From Actor Using Scripted Actions - Using an editor utility to batch add and remove components from actors in a level using scripted actions and subobject data subsystem
Add a component with Blueprint script in the editor - An official example using subobject data system where the same basic logic can be applied for deletion.
Unreal 5.1 python edit blueprint components - An example editing bp components with python
Please let me know if you have any questions!
Regards