Lately with warmer temperatures I've been running one overnight burn a day. Light 20-25 lbs wood 6pm and it burns until 9am or so next day. I've found that if the morning temperature rises quickly the cat will stall with a few small pieces of wood left. I've been bumping the stat wide open which makes this wood relight and burn off.
My question is should I open the bypass when I do this? If I find it stalled I leave the cat engaged and open the stat. It might go active again briefly as it burns off then go inactive.
I just don't want to clog it or damage it.
Are you having weather you expect to hang around until March, or are you passing through temperature regimes on your way from typical fall weather to typical winter weather? If you are passing through some shorties on your way to actual typical winter weather, I would probably not fool with my install. You can probably change the weather pattern that this bumpy troublesome timing thing occurs in by adjusting your pipe height - - but it might make it tricky in typical winter weather which would suck, a lot.
I think you have two variables going on here.
One is how much draft the flue is providing at the cat outlet. You can change it some by adding or subtracting total pipe height, but the absolute suction provided by the pipe is still going to vary with both outdoor temperature at the flue outlet, and the temperature and volume of the exhaust gasses coming out of the cat.
That's one. The other one is how much of the smolder coming off your remaining chunks is volatile, and is the volatile mass per unit time adequate to keep the cat active.
Honestly, given your actual question, I think either is fine.
You can leave the stove alone, let the sun warm up the house and have a pretty fair chance of finding enough still burning coals in the ash bed to relight the stove tomorrow night with no match.
Alternative extreme, you could go to bypass, open the air to wide open, wait a few minutes, open the loading door, wrangle the coals forward - some days get the cat hot enough to re-activate and sometimes not. All assuming you have the time to run this in the AM.
Thankfully your dilemma is a short blip in my burning season. I pretty much don't open the loading door unless I am going to reload with all the wood I can possible cram in there.
I did have a few days back in late August when I would just leave the stove alone in the AM and have coals available to restart after work. It was 8-20 to 8-23- 2015.
Then it got a little colder -sounds like you are kind of here right now- where I too wanted those last few BTUs in the AM to warm the house up a bit before my wife gets out of bed, and then let the stove go out while the sun is shining and the last of the Canada geese get out of town. Twice I did load the stove closer to bed time instead of right after work so I could catch the tail end of the burn in the AM and open the air control before the cat got to inactive.
I do remember one morning in this weather pattern I was able to go in to work a couple hours late. I had ash bed all the way to the back of the stove, two splits at the very back glowing kinda bright, about two baseball bats worth of wood back there. I went to bypass and opened the air control; a few minutes later I stepped out to check my flue and products other than steam were coming out of my stack. (Newly regulated burner this year, I'm sure I am obsessing). When I got back inside I found flames coming off my two splits back there, and the cat hot enough to re-engage. I re-engaged, checked my flue again a few minutes later and was back to a steam plume.
Probably more than you really wanted to know, but really I think there are too many variables to expect the system to run the same in three different seasons.