I have the same issue. I have engine from github (5.0.3 release branch) and i builded it with Development Editor Win64 configuration. Then, i opened my game and everything is good untill i start to package it. When i start to package my game, a lot of engine related object files *.obj comes to my game intermediate folder. Additionally this process takes huge amount of time and i can’t understand why it happens. As @Ciprian_Stanciu mentioned above, my engine from source hasn’t object files for Development and other configurations. Only for Development Editor configuration. And may be because of that when i packaging my game, solution can’t find Development Game object files of engine and start to build them.
The question is how to fix it ? because normal engine from launcher working correctly and has prebuilded obj files for Development and Shipping.