Yes the MS compilers unfortunately don't support some basic features. The easiest thing to do is to disable those patches that don't build and then look at which ones you want to get to work with.
patches.cpp is intended to be hash-included from PatchRegistry.cpp, it's used along with includes.h to determine which patches are included. So if the compiler tries to compile patches.cpp on its own it will fail - remove it from your build if necessary. Then simply comment out those lines in these two files that you don't need.
As for the FLAC dependency, that must be from Juce. We generate the build scripts using Introjucer, are you familiar with it?
It might be time to revisit the OwlSim windows build. Let me know how you fare!