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fermenting Smoking my mash pre or post ferment?

During the summer I freeze my chilli crop and then make a huge batch of hot sauce at once, fermenting a mash for several weeks. But last year as an experiment I smoked some fresh peppers before fermenting and also smoked some completed sauce. Both experiments worked great and I now want to smoke all the chillis from last years crop to make this years sauce.

My question is to ask if anyone has smoked their chillis directly AFTER fermentation. As I have a fair few kg of chillis to process I think it would be easier to do it after fermenting (put the fermented mash in a tray and stir a few times during the smoke) but I would like to hear of anyone's experience of doing something similar - I am concerned that the smoking this way round on the fermentation would have an adverse affect. I would add that as part of my sauce making process I add vinegar and simmer gently for a few minutes to stop the fermentation process.
As far as fermentation science goes, what you’re doing is fine. Once you cook and-or add vinegar, the fermentation process stops. That’s good news in your case, because you can basically make this more of an art project than a science project. Taste test.