Sorry I don't have a time-out issue so I can't help you with that. Maybe the php settings of the server have something to do with that.
As of the symlinking, it can't corrupt your files because symlinking can be more or less compared with creating a shortcut in windows. Only you make a shortcut to another directory.
But I just think of something, it could be advisable to move all files to the new directory first because all downloads will get in that new directory.
Files can not be corrupted, but it is advisable to make some test directory's and test with it first, so you can see for yourselve how it works and what it does, so you get more comfident about what you are doing.
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