Hi,

It sounds like you are using File>Open>Arduino Project. That does sound a bit confusing if you selected the sln. Currently if a solution is already open that feature will open the sketch into the currently open solution, it also creates a project if one does not exist.

If you simply want to open an existing Arduino solution then either close the current solution and use "File>Open>Arduino Project" or use the standard File>Open>Project command to open the project or solution. The latter will add the solution/project to the recently File used menu

So, the Arduino menu items are for new users (or people who don't care). Once you have a project and solution, you can open them as normal vs/atmel project/solution. The plugin does not mind how these things are opened so I recommend using the standard ide commands.

I hope this helps