Is this partial upgrade safe to do?

whether partial upgrade is safe or not depends upon which packages it's holding back.

• If it's a app you have installed and is not important for the system to run properly, the partial upgrade is safe.

• On the other hand, if it's holding back a package which is essential for the system to work properly, partial upgrade is likely to break your system.

It is better to hold on, have a look at the packages been hold back, and then fix them(either by removing, replacing or installing properly).

Just to add citation for my answer, the Ubuntu wiki on partial upgrades syas,

If you use Update Manager to upgrade your packages, and it offers to do a Partial Upgrade do not accept it without thoroughly checking what packages it offers to remove, upgrade and install. If you do, you will most likely end up removing packages that shouldn't be removed, and waste time and effort repairing your testing installation and asking for assistance.

I found the issue a while back and never posted the answer. The problem I was having stemmed from the fact that I overwrote the nautilus executable with nemo, so that all apps would open nemo instead of nautilus.

Uninstalling nautilus, removing the nautilus executable, then reinstalling nautilus fixed the problem.