Seen multiple reports that the Windows 10 Anniversary Update deletes other partitions (containing Linux installs) without asking. :S— Alan Pope (@popey) August 3, 2016
Another Twitter user says that the upgrade deleted everything on their non-Windows drives (we're not sure how many there were) without asking:
Aggggh. When I installed Windows 10 it deleted everything on my other drives without asking— H5S (@TheH5S) August 2, 2016
Clearly, this is enough to cause anyone dual-booting Linux to think twice about upgrading. It also highlights the fact that backups are extremely important before upgrading an OS - especially Windows, as Microsoft has never held competing partition formats in high regard.
So, what on Earth is going on here? We're not entirely sure at this point, but we do have a couple of theories. The first is that Microsoft might not actually be deleting the hard drive data, but instead is corrupting their partition tables. In that event, a tool like TestDisk might be able to be used to help recover the data.
A tool like TestDisk might be able to help you recover lost data
If data truly is deleted, TestDisk still might be able to offer assistance, or any recovery tool that fully supports the Linux filesystem that was being used (eg: ext4).
What's unclear at this point is whether or not this update can affect hard drives other than the boot drive. By all appearances, the main risk is if you are dual-booting both OSes on a single drive. What could also happen is that the boot-loader (eg: GRUB) could be overwritten during the update, which will require users to boot into a live Linux environment to re-write GRUB (or another boot-loader) to the drive again, allowing them to then reboot and actually access their Linux install again.
If more important details trickle out, we'll update you. In the meantime, if you are a user who installs Linux and Windows on the same drive, we'd recommend staying away from upgrading right now, until more confirmed failures or successes come out. And always, always backup your drive before upgrading. This issue proves that not every upgrade will go as smoothly as it should.