Do messages like this annoy you?
Do you wish Eclipse would just fix the problem, refresh the file, and let you edit it?
If the answers to these questions are "YES" then I invite you to comment/vote on a bunch of Bugzilla entries that we are discussing these issues on.
Bug 14867 - Don't force me to refresh all the time
Bug 303517 - Update IResource sync state in a timely manner when discovered out of sync
Bug 337446 - Text search should handle out-of-sync resources