Yes, this started happening to me on 5.3 as well. Every time I start my engine it deletes my Enhanced Input nodes.
It was fine since 5.3 came out but this started happening today.
5.3 also deletes my GameplayMessageSubsystem nodes. I fixed this by opening the uplugin file and change the LoadingPhase for all modules with BP functions to PreDefault. Both of these problems started at the exact same time.
Verifying my engine files did not help.
I fixed both issues by opening the uplugin file and change the “LoadingPhase” for all modules to “PreDefault” instead of “Default”.
I found this solution from here Unreal Engine Issues and Bug Tracker (UE-158125)