It's very likely a small issue such as hand interference that slipped through the QA tests. They make a lot of these and it's bound to happen but, sad for you that it's your watch. They have a good reputation and mine, for example, has been faultless for 20 years from new. It's hardly a cutting edge calibre so, there is not an underlying design fault, just that yours has an issue.
I'm surprised they offered to change the watch but, I'd just do that and write it off to experience.
It sounds like it is 75% wound when it stops so, it's probably a small interference (probably the hands - what time did it stop?). When you start winding it again, you are just dislodging it slightly and it starts to run.
Runningthe chrono should not dramatically reduce power reserve. The extra moving parts need a little more torque from the spring to run them so, it will stop before it would without the chrono simply because as the mainspring torque reduces close to the end of the wind, it cannot overcome the resistance of the basic calibre plus the chrono. Nowadays, mainsprings are designed to be as close to constant torque as possible so, it will be close to the end of the reserve anyway.
Good luck, whatever you decide to do.
Regards, Chris
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