not sure i understand the question here, but i can try to provide some info.
16.09 corresponds to Linaro releases 'naming', which we tend to make every 3 months or so. Each Linaro release is based on Debian. So far we have been using Debian Jessie (aka stable) exclusively. Debian 8.6 was 'the current' Debian Jessie version when we released 16.09.
It is usually fine to upgrade the user space packages with
It should work 99% of the time.
Couple of notes:
* in the next release we are planning to start using Debian testing, instead of Debian stable
* it is not possible to upgrade the kernel with apt-get upgrade (at least not yet, we are willing to change that in the future).
* reinstalling/flashing each new release every 3 months is possible, but it will wipe out your eMMC