Depending on the silicone used and its chemistry, it could actually be producing ammonia as it is curing. That and GE silicones contain petroleum distillates for mildew resistance (though many of their products don't advertise this). If you're not already running a skimmer, do so as aeration is the only way to remove distillates if there are some.
+1000 on bacteria stability. MB7 is great to get the bacteria going again. Take it slow though.
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