I am not sure this is the right place for reporting a bug which it is present in version SB 8.0.0, until (at least) in 8.0.2.
I did not check in 8.0.3
If you assign a customised Key Binding sequence to:
File → Export Run Only → Application (Apple) it stays until you quit SD.
If you quit and restart SD, the same sequence combo is re-assigned to:
File → Export Run Only → Application (Enhanced).