I have just hit this problem for the 1st time. In my process I develop with hot-reload too, to ‘fix’ the issue I loaded each of the affected BPs into the editor and Selected Refresh all nodes, then saved the BP again. This cleared the issue for me. No recompiling, or cleaning the project files etc. Just loaded editor, the two BPs, refresh, save.
I have noticed that 4.16 (version I am now working with), doesn’t complain about unmatched dependencies like 4.13 would do (engine we have just moved from), when updating the base C++ for a BP.