Your HVAC contractor needed to submit a load calculation with the permit application that determines the size required. Was a "real" calculation done or were the numbers just expediently faked to come to an outcome? It's very likely that whatever was put in 50 years ago would not be considered a proper size with today's standards and concepts.

If the permit application was incomplete, I wonder if the person who submitted it knows what they're doing?

Don't be in a hurry, it's June. Getting a wrong sized furnace or not one that you want will adversely affect the comfort it provides. I had such work done in a coastal SoCal location a few years ago. I believe my HVAC contractor submitted the permit request online to a city (not county) jurisdiction and it was granted the next day. Do it right, not quickly. Slow down the contractors on the scene to explain what they're doing and find out what went wrong.

Good luck.

Interesting. Our architect submitted our plans and he consulted with a structural engineer and an energy consultant; we did not have an HVAC contractor and, at that time, we were just selecting our contractor. I will check with our architect about what the city required and what was submitted.

Just to close the loop. Our architect informed me that we do not have to select a furnace now and that the city does not require knowing the ,model. Honestly, I feel like he sent me into a bit of a panic. Our remodel will take 6+ months and we will now have time to research and make a better informed decision.

Now that the pressure is off, you can step back and analyze all of the HVAC needs. Installing a furnace in the attic is not the best location. Is there no room for a utility closet? Is the current duct work in the attic? If not then is the architect responsible how the new duct work will be connected?

we won't have access to the unit to change filters

You can install a filter at each return. However you still need access for a technician to climb into the attic to service the furnace. I suggest to allow adequate space around the furnace and good lighting for servicing.

there's also an AC unit on the roof

Does the AC use a separate duct system to cool the house? You need to understand what is currently in place and make a decision whether you should replace the current AC with a split system integrated with the furnace.

THat's a good outcome, too bad about the miscommunication or whatever it was.

There are aspects of HVAC work that are like having a custom pair of shoes made. Or even the work of a remodel contractor. Standard materials are ingredients used by a knowledgeable tradesman to craft a custom tailored, one-off installation. Following required standards and accepted techniques to produce the desired end result. An architect or an "energy consultant" can offer guidance or specs, just as the contractor has blueprints to follow, but in the end, it's the skill of the tradesman that produces the result.

Good luck.

Oh, missed the filter part.

Yes, having a flat disposable filter with a hinged return vents for access works fine and is typical for a unit in an attic. My SoCal house is just like that.

Mike, sometimes with flat roof homes, even upscale ones, vanilla condenser units of conventional split systems are put on the roof. They're usually not visible, the ones I've seen do not give the appearance of a cheapo package unit or swamp cooler perched on a sloping roof. Small lots and small side yards, especially near the beach, can lead to that. Even if visible, it may be the only choice.

In the Northeast and Atlantic regions of the country you will may see HVAC equipment on commercial buildings roof tops but not on a residential home. If AC is added to an old home you will see the condenser sitting on a shelf attached to the side of the house. I have seen even this done on new construction townhouses.

I am no expert on roof top residential AC equipment. But I still think the AC should be evaluated and determine if it makes sense to make changes during this major renovation.

I agree, Mike. The residential rooftop installs I've seen and known about use the very same equipment that would be sitting by the side of the house. In situations where there is no room by the side of the house or no out-of-the way area to place the equipment because of layout or lot size, putting compressors on the roof can be a suitable alternative.

I found these photos on the website of the excellent SoCal HVAC contractor I used, showing jobs they've done. This is a residential rooftop install. I wish I had a view and a location as is pictured. Lovely setting.

Because of the space problem some have, a few of the manufactures make an upright model (that resembles a mini-split compressor) for tight spaces. Here's a photo of the Carrier/Bryant model. I have one of these and it really solved the tight space I had to deal with.