Which one is correct—"one of which" or "one of them"?

I think either could work. I'd go with the top - which should actually be "one of whom" - but would change it to read as follows instead:

• This made her think of her Grandpa and her Dad; one who has passed on and the other is deployed.

or:

• This made her think of her Grandpa and her Dad; one has passed on and the other is deployed.

The thing you need is "one of whom." Not too hard to arrange if we speak of just one person:

This made her think of her grandparents, one of whom has passed on.

But it's tricky to talk about both people. Let's try this:

This made her think of her Grandpa and her Dad, one of whom was deceased and the other, deployed.

The sentence "This made her think of her Grandpa and her Dad; one of them has passed on and the other is deployed." is unlikely to be correct since you're combining two complete sentences with a semicolon instead of a conjunction. I wouldn't use a semicolon unless I was providing further information abt the previous clause or elaborating the idea of "this made me think"; which is not really the case here since the second clause contains information abt her grandpa and dad rather than about "this making her think"... whereas the correct sentence would be: This made her think of her grandpa and her dad, one of whom was deceased and the other deployed. Aparente 001 's version is the best one. Add to this, we do not capitalize grandma, grandpa, father .., when they are preceded by possessive pronouns.