Yes, you still own the homes despite having RTO residents and you may end up with a fair number of vacant homes due to default.  

My dilemma is whether I use my VA loan for the multi family which will turn into an investment property after I change duty stations in two years or save that VA loan for my personal residence once I establish more permanent roots upon competition of my service. 

For a primary residence I always recommend cash or financing, not leasing. 

@Chris KinneyAs @Natalie Kolodij said - you cannot deduct interest against your rental property if it is used for your personal residence.

I've used the house flipping calculator here on bigger pockets, although I'm thinking the nubmers would change a little big given the fact that it would be my primary residence for a minimun of 2 years.

Full liquidation of partnershipI feel like we've exhausted all of our options, but still are struggling with figuring out the perfect solution.

He plans to live in the home as his primary residence for 2+ years.

Security deposits and last months rent, I would not normally recommend to spend that on repairs; but sounds like you need a solution.

I have my primary residence mortgage and the rental property mortgage both through a commercial bank in Canada(RBC).

If you submit an offer during owner occupancy only period and do not plan to occupy the home as your primary residence you are running a large risk and would recommend against it.I've heard of investors that did this, then got told on by another investor that was looking at the same property.