Building the solution should overwrite the original binaries unless if the binaries are currently in use by the Game or Engine. If you modify the Engine module you should just select the Engine Project (UE4) and build that exclusively. You can also build the Game module exclusively. If you don’t want to use the debugger (breakpoints etc) then you could delete the pdb files to save some space but then you won’t know what happened when a crash occur.
100GB is like a minimum working with EU4 though.