You have to shut down the sump for a day. Drain it, dry it, install the baffles, wait 24hrs, then bring it back up.
Not skimming for that time is no big deal, you might have to move your heaters up and put in some powerheads for flow.
You can also try a filter sock and other medias to stop the bubbles, but then you have to maintain it, not a good long term solution to microbubbles, IMO.
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