Since this pops up in google searches:
There is the Core Redirects system one can use to achieve this:
For example you have the blueprint MyGame_GameInstanceBP with a variable bGameStarted and you created one in the C++ UMyGameInstance called bHasGameStarted. The redirect would look as follows:
; In DefaultEngine.ini
[CoreRedirects]
+PropertyRedirects=(OldName="MyGame_GameInstanceBP_C.bGameStarted", NewName="MyGameInstance.bHasGameStarted")
Note the addition of _C to the blueprint name and the ommision the U prefix for the C++ class.
After adding the redirect, you can delete the Blueprint variable and all references to it will be remapped to the new C++ variable. As long as the original variable is still there nothing will be remapped.