Depends. If you have the clear, two part epoxy that's branded "JB Weld", you're good. If you have the actual JB Weld originally intended to bond metal surfaces, don't use it - it has zinc and aluminum particles in it.
That should be OK, since I doubt the company making JB weld would be adding anything to standard 2-part epoxy putty. However, keep in mind that some of these products do contain an anti-mildew agent, which would be very bad for a reef.
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