Just to make sure I understand the issue: So the original project was set to use compiler version 4.9.1, (ie) the Eclipse project files contain references to 4.9 compiler. Now when you set it to use compiler version 5.1.1, are you saying that the .cproject, .ccsproject files do not update to reflect v5.1.1?
If they do not, then there is likely a bug. Are you able to zip up and share the project with us so we can reproduce the issue? If the project is too large or cannot be shared, please send us all the project files (.cproject, .ccsproject, .project) and we will see if that is sufficient to be able to reproduce the issue.