Visual Studio needs to make non-functional changes to this project - visual-studio-2010

I have a visual studio solution with a a vs2010 project
Everytime I open it I got this warning.
Visual Studio needs to make non-functional changes to this project in
order to enable the project to open in this version and Visual Studio
2010 SP1 without impacting project behavior.
ANd it generates some xml log files
I need to definitely convert it to vs 2012
How can I do that without breaking anything else?

I was able to solve it by opening the .csproj file and changing this
<FileUpgradeFlags>0</FileUpgradeFlags>
for this
<FileUpgradeFlags></FileUpgradeFlags>

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From your comment, it seems you are trying to debug an opened file/folder right?
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Instead of closing and re-opening Visual Studio have you tried, unloading and reloading the project (.csproj) which imports the shared script? You can do this from the Solution Explorer in Visual Stduio by right clicking on the loaded project and selecting unload and then on the unloaded project and picking load.
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