More info: This occurs just occurred again with the following steps with nothing checked out to begin with.
1 - opened an unrelated test list
2 - changed the order of the tests in the test list
3 - selected OK on the edit test list dialog
4 - while trying to check out the test list from source control, test studio popped up the dialog that it lost the connection to source control.
5 - I immediately reconnected the project to source control without doing anything else.
6 - I saved and checked in all changes that Test Studio made when it disconnected.
7 - I viewed the changeset sent by Test Studio to TFS which included the test list change AND the deletion of 32 tests and a test folder even though all of those tests remain on the Test Studio client.