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Specifying a linked folder for the project build output folder will delete any content already existing in that folder. Repro: Properties->Java Build Path->Default Output Folder->Browse: Create New Folder (Enter a folder name) Advanced->select "Link to folder in the file system" (enter an existing folder path which contains nothing valuable) OK->OK->OK "OK to change output folder location...remove all from old location" prompt...answer doesn't matter. Build of project will delete contents of the linked folder. Subsequent builds will not delete any existing contents of the folder.
Remove "all from old location" is a question to remove class files from the current output folder location not from the one you are specifing right now. Moving to JDT/Core for clarification since they control the output folder.
By default, we consider owning the output folder, and will clean it when rebuilding all binaries. You may turn this off: Preferences>Java>Compiler>Build Path>Clean output folders on full build.
