Yes, this does indeed appear to be a partitive genitive.
Changing the word order as you suggest is legitimate if it helps you.
I think it is most useful in its original place where una and sine alia are next to each other.
I like analyzing things sequentially, so let us start with the whole sentence.
To clarify the role of the relative clause, I will add another comma:
Sane rerum, quae realiter ab invicem distinctae sunt, una sine alia esse et in suo statu manere potest.
To better grasp the core message, we can ignore the relative clause which gives additional detail:
Sane rerum una sine alia esse et in suo statu manere potest.
Let me also drop the other half of what can be done:
Sane rerum una sine alia esse potest.
Now the message is clear:
Clearly one of the things can exist without another.
If there are only two things, then "the other" is better than "another".