The Cottage Smallholder

I've just made Green Tomato Chutney with Delia Smith's recipe 9which turned out really well last year). Recipe gives about 4 hours simmering time, but after more than 5 hours there was still more vinegar than I would have liked, and I was worried it would getting overcooked and too mushy. Plus I was fed-up and it was midnight by then! So I bottled it.    But there are some small pockets of vinegar (little fingernail sized) in the jars.  I'm hoping they're going to be absorbed/evaporate during the 3 months' maturing period. Anyone else had same problem, or got any words of optimism or advice?