Depends on what was changed between the builds. Nightlies are made for testing purposes without additional considerations regarding upgrades.
apt upgrade will affect the kernel, DT and board support package, but will not affect boot script changes, default package list changes and some build time tweaks.
In the end if you are using nightly images not for testing purposes it's better to not upgrade the kernel and DT unless you need something specific that will only appear in the newer kernel. For example due to ongoing migration to kernel 4.11 DVFS will be broken on H5 boards (including PC2) if you update from earlier kernel.
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