What type of solder are you using?
What type of soldering iron (and watt output) are you using?
I've never needed to actually clean the board for this operation, but I have used acetone to remove the conformal coating at times, when I needed to do so.
While it is possible to overheat the board, it would take a LOT of heat to do so. I have my soldering station set to just under 400*C, and many times when I'm de-soldering something like this I will turn it up to about 450-ish.
While I usually use a good solder sucker for this, I have found that sometimes solder wick works better.
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