When I made red pepper and tomato chutney a couple of weeks back, the recipe told me to simmer for 2 hours. After 2 hours it was still totally liquid so I just kept going. In the end it was 5 hours in total before I thought the consistency was right. The end result is just fine. So trust your instincts and cook it as long as you think it needs -- there shouldn't be any "free" vinegar in it. A recipe is only a guide, and it will vary according to how ripe/juicy your veg is, how slow your simmer, the size and shape of the pan ...

It does thicken a little when it cools, but if it's still liquid I would cook it some more. According to Fiona, who knows more about chutney making than I do, if you cook it long and slowly, it doesn't need to mature so long in the jars before you eat it.