This might not be the right way to do it but it removes the error message.
- Right-click on your project.
- Select Team->Synchronize Workspace.
- Go through the compare view of each file and then update your local file accordingly.
- Then, right-click on the file, click on Marked as Merged.
- Back to project view, right-click on your project and select Team->Merge.
- Right-click on your project and select Team->Push to Upstream.