Catrin, this is a really normal pattern of recovery. Try not to get discouraged. Neck rehab never goes along smoothly with the patient recovering at a nice steady rate without any exacerbations and episodes pain recurrance.
There are two good signs hidden in your story.
1) The pain didn't start until that night, so there was irritation but not enough to be painful while on the bike.
2) This happened only after your second consecutive day riding.
Your muscle were fatigued after the first day and they couldn't do as good a job of stabilizing your neck the second day, leading to some stressful posture and or unwanted motion in your neck while on the bike. As your muscle endurance improves, this will improve.
So here is some advice.
Cut your neck some slack, it's trying to build up some strength but it can only do it so fast. Think of what it's like to train for a big event, you have to work into long distances slowly so that your body can adapt and grow. Your neck muscles are doing the same right now. In the meantime, if you overdo it, it will hurt occasionally but it just means you need a little recovery time. It doesn't mean your heading back to square one.
You should be doing some postural strengthening exercise/movement control exercises for your neck every day. Did your PT give you some of these? Make sure you keep doing them. On the days you ride, do them after your ride and not before.
Rides should be judged by time out on the bike not miles. Your neck has to hold your head up regardless of how far you're riding and how fast, so the way to progress is by time, not miles.
I hope that helps.
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