An update to my previous problem with Sync From Data:
Starting with a a project that is identical to the installed files, so it shows up green. The Sync From Data option is greyed out, as expected. I then delete a file installed by that project, and switch back to WB. A quick refresh box pops up, just for a fraction of a second, so I suppose WB has noticed there has been a change. However, the project is still green, and the Sync From Data option is still greyed out.
If I then close down WB and reopen it, so that it rescans the data folder, the project now appears with the yellow checkbox, showing that there's a difference, and the Sync From Data option is available. After Syncing, the option is again greyed out. If I then go and edit a file installed by the project, once again the project stays green and the Sync option remains greyed out.
Hope that helps.