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Update 2 (fixed):
I decided that i would remove all books from the device, to see if it was one of the books that was messing things up. I removed the books through calibre, but I was surprised to see that even though some books were supposed to be removed, they were still on the device. There were also empty directories (authors).
I removed these empty directories and the books that calibre did not detect through explorer.
Once the device was empty it would no longer hang once disconnected. I then started the process of re-adding books. Some at a time, disconnecting and letting the device update it's database every now and then.
At the moment the device is working as intended when disconnecting it from my PC. I'm still not sure which book (or whatever it was) that caused the problem. The only thing I've noticed that has changed is that the cover of the book I am reading at the moment no longer fills the screen completely when the Libra is in power save mode (despite no changes done to the cover).
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