What's the manufacturer and model of them? Perhaps we can look up what the motor is capable of doing...

Distributed by J&D manufacturing, but the unit bears the name - Mulitproducts. I will likely call J&D on Monday to ask about this.

It seems to me, that the most simple solution would be a switch on the electrical line to the shutter motors. When you want to by-pass the motors, just flip the switch and avoid the issue altogether.

Birdwidow, I thought of that, but had already wired it - though I don't think it would be that much of a problem to cut into the line and rerun part of the wire. That may be what I end up doing - I want to first see how it works (once I energize it) and see if the manual by-pass with a second chain remains practical. I also thought of simply turning the thermostat way up before I utilize a by-pass so they would not turn on.
I have the shutter motors hooked up to a dual stage thermostat and down line from there I could put in another weather box and switch. I put in several weather boxes in a line on one wall. . .the first is a GFI outlet, then the thermostat, then a line to the motorized shutters and on to the next box which houses the variable speed control for the fan. I think your solution is the most logical one. . .I would just have to remember to turn the switch to off before I engaged the by-pass. Or, when I talk to the mfgr on Monday, they may tell me it makes no difference if they happen to come on while I have by-passed them.
By the way, for general info for those in the forum, I had opened both 16" shutters manually while I was working inside on other things - and I had already installed outside of one of them one of those attic vents - louvered and screened. The other one was just open the outdoors without any vent. . it was amazing how much of a breeze came in the one without the louvered vent compared to the opening with the louvers. So, I have decided to take off the louvered vent and protect the opening from the weather in another way. . . The air flow restriction would not likely be as much with the exhaust fan on, but it really made a difference when it was just open for the breeze.

Update: I contacted the mfgr this morning regarding my question in the initial post here. Apparently there will not be a problem hooking a second chain to the bar which is attached to and opens the shutters and use that for a manual by-pass. The shutter motor arm - if it is hooked to nothing - will simply go around and around. If it is hooked to the shutter bar (which is held in a closed position by a spring) the motor will start when energized but will "stall" when it has resistance. So, if I understand all of this correctly, the resistance will be met even if the shutters are already open and will stall. Nevertheless, I will test this out carefully beforehand to see that this is correct.

Zacman,
It appears that you are going to go the manual operation route but if you do decide to rewire I wanted to mention that I am doing some wiring for a louver and just like my exhaust fans I have multiple switches. I have a power shutoff switch just inside the entrance door. That does the opposite of what you want because many times I just don't want things open for different reasons, usually just to close up a little sooner in evenings when cold nights are forcast. You need to remember to flip the switch back after the temperature drops below thermostat settings so you are set for the next day.

For the thermostat override switch I usually locate those on a suspended board (barely reachable)just below the thermostat. I actually use that switch far less than the cutoff switch.

Bmoser, thanks for info. I ran two fused 20amp circuits to the gh - and ran one circuit to each long side of the gh. One side where I would put the heater and have outlets for other uses, and running to the other side for the fan, louvers, light, and other outlets. After I did this, I realized that the cut off at the fused panel was 40 feet away at the well, and due to 8'high chainlink fencing around garden perimeter, was really about a 120' walk to get to it. So for convenience I wired, just inside the entry point, a 4x4 box with extender and put in a 20amp switch for each circuit - giving me the option of cutting off either of both circuits. So, I can use this cut off to cut power to the louvers, except that if it is at night, I cannot cut off the motorized louvers without also cutting out the light, but I can plug a trouble light into an outlet for one of the other circuits if I need to. So I should be OK, though I will try the manual by-pass out and see what happens. The manual by-pass was simple enough, just another chain to an s-hook at the louvers, with the other end having a small key ring hooked to it which I can pull down and slip over an eye-hook. I hope to finish my outside light pole (12') for light outside the greenhouse and for the adjoining raised beds today and will then test everything.

I bought a J&D vent with motor just like you have. It worked three weeks before going bad.
It stripped the gears that apparently were made of plastic.

I sure hope you have better luck with yours than I had.