Is the .glyphs file placed in a Dropbox folder (or was it accessed by another app, or TimeMachine or Versions)?
Verify that your write permissions for the file are still OK.
no, its on my computer and there is no access by another app. its all happened after the latest update.
the problem is, its happening time to time!
The orange is a layer color. You can change it by holding down the option key.