While ships are in either overhaul state, do their maint clocks stop?
They stop if a ship is in orbit of a maintenance facility or undergoing a minor overhaul. They rewind during a major overhaul.
And is there a way to get the clock reset faster than at 1/4 time elapsed?
It will be boosted by the logistics bonus of the planetray governor. So a 30% bonus = rewind at 5.2x
IE I have ship with lots of spares. It goes out for 2 years, comes back does a minor overhaul to reload spares, goes out for another two years. Now it needs to spend a year in major overhaul. Seems kinda drastic. But it may be what you are aiming for.
That is correct as things stand now. I might adjust it based on playetesting in v2.3 but that is probably better than reality in terms of how long ships are in port compared to deployed. The big difference I have found over the current system is that you can put ships in for overhauls whenever it is convenient. You no longer have to wait for free shipyards and you don't have to wait until the ship is falling apart because of the old fixed cost approach.
The side effect then is that you basically need to add more ships to your fleet to maintain a given number of them active at any one time. Which in itself is okay, but runs counter to the rest of the Aurora philosophy of minimizing the size of fleets...
In many cases, warships will be in orbit of fleet bases anyway so they won't need to spend time in overhaul because their clocks won't move and their spares won't diminish. A ship will be spending about 25% of its actual deployed time in overhaul under this system, which isn't a lot more than before. You will therefore need say 25% more ships than you think you will require at any given time, although you can pull ships out of overhaul in an emergency.
A typical warship might spend two years sat in orbit with nothing to do and no change to clock or spares. Then it goes out on a one year mission, returns and spends three months on a major overhaul. In this type of scenario, which I expect will be common, the ship is spending three months in overhaul over a period of 39 months. Ships like survey ships or terraformers will probably be the ones spending the highest percentage of their time in overhaul because they are often constantly on deployments. It therefore seems reasonable that they will be the ones most often in yard hands.
Steve