If you install version 3.5 into a different program directory than version 2.x, version 3.5 will not have a record of your old projects. You can still open them.
To open a version 2.x project, use the Project > Open Project command. In the dialog box, click the Browse button, and navigate your way to the old project's .PR file. Select the old .PR file, click OK, and then click Open. Source Insight will begin converting the project to version 3.5 format.