First of all would be good to do it for release 3.0 as there were already related changes in trunk (ZBXNEXT-1263).
After the ZBXNEXT-1263 there are much less differences in source file names regarding architecture (x86 or x64) which is nice itself, but the task is not complete

I suggest to:
1. rename "build" to "build-win" or something like that.
2. move "examples" and "include" folders one level up, i.e. to the "build-win" folder.
3. move content of "project" folder 2 levels up, i.e. to the "build-win" folder
4. remove "win64" (together with the dummy README) folder and "win32" (together with empty "project") folder.
5. Some source files should be reviewed to reflect location changes.

This way it will be more simple, logical and clear for end users what is what.

This idea came to me when I worked on an idea to describe in a user friendly way how to compile zabbix agent on windows (in ZBX-8054) with a final goad to officially document that (for 3.0 doc only).