If you already got it using Tortoise then it should be ok. Possibly a problem with the MS SQL .sln file. I would try using the regular mojoportal.sln and rebuild the solution, as long as you have Debug or Release as the build profile it will use MS SQL.
Updating from the repository only affects files under source control, it won't affect any files you've added under /Data/Sites/1/
Hope that helps,
Joe