I activate a mylyn task in the morning when I first get in to work. Later I open files using "Open Resource" via ctrl shift r. A bit later in the day I find that files have surreptitiously closed without me doing it. This also happens sometimes in the morning upon activating, but I am not sure if I just didn't see what happened to the task the night before. It seems that perhaps files I haven't opened in awhile are automatically closed, so lately I have been opening the file tabs at least once a day to keep them around, although I am not 100% convinced that this fixes it.
Also, as a corollary, sometimes mylyn folders disappear from the task list in the morning when I start up eclipse. It seems that if I do not deactivate all tasks properly the night before, in the morning either the folders all disappear or files are listed from one of the tasks but no mylyn task folders are activated. If I am not careful, if I open up the wrong task, then the files get mixed up and I have to manually correct the issue. If I click the mylyn view, and click the far left mylyn button, I can select "restore from tasks from history" and pick a date from EOD of the day before, and the folders are restored, but I don't trust this. As protection, I have been backing up the .mylyn folder from the workspace on a thumb drive. Is this functioning as designed, or is mylyn broken?