Seems that laptop-mode-tools should fix this as read in Changelog:
-Set HD power management values to 254 instead of 255. Some hard drives go into 
"no power management" mode only on 254, while 255 yields some kind of default 
that you don't want.

http://www.samwel.tk/laptop_mode/changelog

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High frequency of load/unload cycles on some hard disks may shorten lifetime
https://bugs.launchpad.net/bugs/59695
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