Window > Preferences > General > Editors
Uncheck the box for Close editors automatically.
You might also want to try installing Mylyn to manage related files in a task context
(eg., to have all the files relevant to a bug or work item grouped such that when you
enable/disable the task, files will be automatically reopened/closed. Mylyn also lets you
filter your Project or Package Explorer so you only see the files you care about at the
moment.
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