I'm facing the same situation with a unstable system after trying to update. Having spent a lot of time into troubleshooting and expecting that community support for this device at least will not get better I am also looking for an alternative.
Looking for an alternative board is also not that easy because the size (nano-ITX) is not widely spread.
Furthermore one requirement for me would be very common hardware/architecture to not depend on special linux distribution, so getting a good mainline support.
These days was the release of a new Odroid x86 board "H4" which comes with 4 Sata-Ports. The board physically seems to fit into the Helios64-case but maybe requires some adaption to different hole-positions.
Did anybody else already considered that as an option ?