I had this problem with my own blueprints, so I think it is just a UE4 bug. Luckily in my blueprint I didn’t have to many references to the variable that failed to import, so I could just delete it and replace it and where it was used. That fixed it.
If it is possible to delete a variable, compile, get the errors, right click on one of the get/set nodes for that var and make a new one, it should work. Hopefully you didn’t get too far into your project. 
Test the above out on a test variable first before you try it on the other used variables. It would be a shame to have to go back and find all the old references.