I have made Cherry ale around Christmas for several years. This year I forgot to add the cherry extract at the 2nd fermentation, so I added it when I added the sugar prior to bottling. Will this affect the taste? could it have effect on carbonation? My beer this year is flat and has an aftertaste that I don't like.
You should be fine adding the extract at bottling. Consider the bottle conditioning as an extension of the secondary ferment. I had a lager that got a yeast taint in the secondary. I added raspberry extract at bottling. It wasn't just a "save" for a lost brew, it turned out to be a fantastic "Lambic' style beer. Kiwi Bruce
This is not only fine, but many recipes recommend adding extract at bottling time so that you start with a small amount, taste it, and add more to adjust as needed. For example, see Jamil's Chocolate Hazelnut Porter from Brewing Classic Styles. You can use a medicine dropper, liquid medicine syringe (for children or pets) or pipette to take a measured amount, mix it into the bottling bucket, take a sample, taste, and add more as necessary. It can be difficult because after a few tastes you often stop being able to tell the difference and can add too much, so I'd take notes and err on the side of less.
It should not affect the carbonation in any way. If your beer was flat, that's very likely a separate problem with several possible causes including:
- temperature - too cold with cause yeast to go dormant
- not enough priming sugar or priming sugar not thoroughly mixed throughout the beer
- unhealthy/dead yeast
A bad aftertaste could have lots of causes also, bad/spoiled extract, infection, etc.