It may have lost it's "Use and Occupancy" permit.

It's not uncommon for occupants to strip the property or trash it on their way out.

I also know that there have been changes (and could be future ones) that restrict STRs.Here's my dilemma: I see some suitable properties but they need to be MTRs and it's unclear what my occupancy rate might be. 

Folks, the OP is an owner occupant, so I am not certain an ESA is "just coming in." 

So, my question is, do loan companies require payments to be made on your mortgage while renovations are being made and therefore your property is vacant, or can you defer those payments until the renovations are complete and you have an occupancy permit?

Another option is to split the cost based on the number of occupants in each unit but this also means you'll need to adjust the charges as tenants move in/out, so it requires more work and I wouldn't recommend it.

Being new to this we are curious as to how we would buy another property after living in the fourplex for a year and a day in order to meet the occupancy requirements.

This time of year, usually early fall, you will find lower occupancy rates.

Never assume 100% occupancy.  

So in regards to the occupancy requirement, after reading the language on a few sites, it looks like there is a misconception of the occupancy period.