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fermenting Post Ferment - What to do with it

I had a 90 day ferment with yellow scotch bonnet peppers in two large mason jars with air locks.
    - 10 percent weight in sea salt thrown in the processor with the peppers
    - I had to keep adding water as kahm yeast and mold kept forming on the top
I finally decided to try out my fermented peppers.  I drained both jars and cooked one jar (rolling boil for 10 minutes, simmer for another 20 minutes).  This turned the mixture almost black - I threw that jar away.
With the second jar, I made one small batch of pepper sauce just to see how it tasted.  I put a new mason lid on the jar with the fermented pepper mixture and put it in the fridge.
Within 30 minutes the top quarter inch of the mixture turned grey.  A week later the top inch and half is a dark grey colour.
Is there a proper way to store the ferment (once I've decided I no longer want it to ferment)?  Or do I need to use it right and away....make sauce, cook it, bottle it etc
It shouldn't be fermenting at all now. At this point it's aging. The fermentation would have stopped after a week or so. If you've still got considerable CO2 buildup now, I'd start asking questions about what sort of black magic you're dealing with. 
Generally speaking aging for longer is always going to help it taste better...
... but it can be risky if you're openning up the jar periodically. 
Safest bet to slow things down and keep it safe is to add vinegar, assuming you plan on using vinegar in the final sauce anyway.