It's a kind of cement used to improve the physical stability of large components. Without it there is a risk of vibration tearing the solder joints apart, especially on large components like those capacitors.
Usually it is harmless and as long as it isn't burnt black it doesn't have any side effects on the circuit. If in doubt, scrape it off, the chances of the the board being moved in the future are probably a lot less than when it left the production line and got shipped half way around the World!
Can you show a close up picture of the board around the damaged diode please.
Brian.