Yep I know what the problem is. There are some things for us to tighten up in the next release but you can fix this easily enough.
The problem is visual micro getting confused in it's temp folder because both projects have the same name. In an attempt to speed up compile vm caches the builds but at the moment the cache it based on sketch name.
The menu item "Build>Clean Solution" somtimes fixes the problem but it is safer to use a different sketch name.
There are some important rules to follow when you rename your sketch. Here is an example of what I did.
1) Renamed folder MultiWii_2_1 to MultiWii_2_1_a
2) Renamed master sketch MultiWii_2_1.ino to MultiWii_2_1_a.ino
3) Deleted the visual studio .vcproj.. files
4) Deleted the vs solution files (.sln) if they exist
Then you can "File>Open>Arduino Project" and vm will rebuilt a new sketch project.
The only reason for deleteing the project and solution is simply because vm will re-build them when you open the sketch. Saves you being burdened with loner instructions
Interestingly enough it is planned for a simle sketch rename function in the next release.
Look forward to hearing how you get on.
ps: Strange your reg email bounced back, that email address has been fine since