I think you just need to step back slightly and first study how the ide works.
It sounds like you are just opening random .ino files and not allowing a visual studio project to be created for each sketch.
In Visual Studio we have a Solution that can contain one or more projects. We can have as many solutions as we like. In your case I suggest you just have one Solution but add two projects to it...
I suggest you click "File>Close Solution" to have empty IDE or the default Solution with nothing in it.
Then click File>New>Arduino project. There are lots of ways to create an arduino project but this is good for our test.
Now you have a Solution with one project in it.
Next, click File>New>Project again and make a second project in the solution.
You now see two projects in your Solution each with one .ino file.
Clicking one .ino file so that it appears in the editor and setting the board (you must select the board in a project to fix it to the project, otherwise we always use the last selected board which can change)
Click the other .ino file so that is appears in the editor, select the desired board.
Now click between the two .ino files and you see the board change.
Do the same for the port. Open/activate the code from different projects and select your port.
Now you should have a board and port saved per project.
If you want to create a project for an existing arduino project then click File>Open>Arduino project. This automatically creates a visual studio project is needed, adds the .ino and other code to the project and then adds the project to the current Solution (or creates a solution for you)
For more information please follow the first steps in our document here
https://www.visualmicro.com/page/User-Guide.aspx?doc=index In Visual Studio do not use "file>open file" to open an .ino unless you just want to view or edit it as a simple text file, without visul micro help.
The rules are that the project, an .ino and the containing folder all have the same name for visual micro to be active. This ensures you have an arduino ide compatible structure to your code. The .ino files can be on the project\sketch folder or in a sub folder calledd \src (same as arduino ide rules)