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I have a piece of equipment with a right angle miniUSB port that went bad. After pulling the old port I have a big blob of solder shorting out the traces.

So obviously I must get rid of the blob before I solder in a new port. The main question is this: using a soldering iron, wick flux, where should I apply the flux before desoldering, to the blob to the wick?

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Flux's job is to clean copper by removing impurities so that solder can properly wet (think "adhere"). When desoldering, you should apply flux to whatever the solder is supposed to wet to. If you are using a copper desoldering braid, then apply a bit of flux to it.

It can't necessarily hurt to apply a little bit of flux to the solder blob as well, if just to help clean it, but the main idea would be to ensure that the solder does not have a coating of dust or other residue on it, such that the iron will make good thermal contact and heat it up properly.

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If you want to remove the blob i suggest you better use a piece of braided cable shield. It will distribute surplus solder on itself. You can add a tiny bit of wick flux on the shield it will make solder more fluid.

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