Users will notice app build times are greatly improved on all platforms, since Emscripten no longer has a two pass linker procedure.
To update Emscripten, I usually do this from the commandline:
./emsdk install 1.39.8
./emsdk activate --embedded 1.39.8
Of course, you will need to rebuild Qt, all other modules and apps.
You can read more about Qt for WebAssembly and Embedded Qt development in the book Hands-On Mobile and Embedded Development with Qt 5