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1. Open a file located in a folder of the project.
2. Rename the folder in Monodevelop
The open file still point to the old location.
If one try to open the file again you get a second file but this one only has the last saved changes since the folder was renamed.
Since the folder was moved within monodevelop any open files should be warning for saving before moving or changed so they point to the new location.
I reported another bug #7202, there the file gone missing was silently closed.
Here it is not closed, but one solution could be to close the file before moving the folder. That way one would get the save/discard/cancel dialog where cancel would not move the folder.
Loooks like this one is fixed sometime before 4.0.2