If you have a web project that is currently deployed to a server, deleting the .project or .classpath files from any Java project which the web project depends on could lead to the deletion of the "/" folder. On Windows, this will in most cases correspond to the drive on which MyEclipse
This bug is relatively involved to trigger as it only occurs if your web project is in a deployed state, either directly or as part of an EAR application and the aforementioned files are deleted. Note that the removal of the files by any means can lead to this issue; for instance, an update of the project from a repository in which the files have been removed.
The only workaround for now is to ensure that these files are not deleted at the same time an active deployment exists.
This bug affects the 9.1 and 10.0 versions of MyEclipse. The MyEclipse
team realizes the seriousness of this issue and is working on a fix which will be delivered early next week for both versions of 9.1 and 10.0. This thread will be updated with the fix details when available.