Let me start off by saying that although we pot a decent variety of products, we have never been asked to do something like this, so this is not based on personal experience. This is just my gut talking here.
I suppose you could use some sort of cap and spray some type of mold release on it so that it's removable after the potting compound is cured, but how reliably would that seal to the board surface? And is that mold release compatible with the potting compound? Some testing would need to be done.
Have you considered using a standard unshrouded .100" pitch header long enough to get the pins above the level of the potting compound? They're available in a variety of lengths and I would think that there would be some off the shelf covers available for them. Even if masking the connectors proved to be feasible, going this route should save some money if it works for you mechanically.
Hope that helps.
Adam
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