Hey Invigor,
I'd strip the new silicone out. It is slowly leaching poisons into your tank. Although it may not kill the animals right away, it may eventually weaken them and shorten their lives.
Recently I was asked to assist an aquarist that was having trouble keeping items alive. Everything in the tank tested good. He had changed water, added carbon and polyfilters, etc. Nothing worked long term. When I asked him about some modifications he made to the sump, it turned out he used a non aquarium safe silicone. I removed it all (and replaced with the proper silicone), and changed the water etc. After that, his tank has run good ever since.
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Van for short
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