1)When you move the files from rootfolder to mapped folder ,still the virtual instance of original file remains as it is for that you need to unload the project
Right Click-->unload the project then again reload.
2)When you delete the Sharepoint Project Items, And you start packaging the solution ,compiler cries 'could not find the deleted file path'.
thus you need to edit the .feature file and remove the guid projectitemreferance and package again.
you need to edit the .csproj file-->ctrl+f-->Find project referance guid as mentioned above.And remove the referance
If you know better way or best practices working with tfs integrated with sharepoint project please do the comments