Well, this was a dumb mistake, I should have thought of it sooner.
Back in the day, when I installed Windows 10 on this computer, I also installed ext2fsd (https://sourceforge.net/projects/ext2fsd/), to be able to access my Ubuntu partition from Windows. Before the upgrade it worked (I was able to manually mount and unmount the partition using this tool) and I was able to boot to Ubuntu without having to fix the partition.
After the update something probable went wrong with the ext2fsd configuration and it started messing up my partition system.
The solution was to uninstall the ext2fsd tool from Windows.
