Hello,
If use BuildTools to update other coin-or projects's autoconf & automake configuration script, the .patch file invoked in run_autotools will cause hunk issue. For the project msvc-pkg, it use this bash script https://github.com/jiangjianshan/msvc-pkg/blob/main/packages/BuildTools/sync.sh to fix them. But a good way to do is to update implementation of run_autotools here. It is recommand to use sed command to do the patch but not use .patch file. Because most of coin-or project may not synchronize the version of autoconf & automake and still using the old version.