I usually soft-mask & grade to match, screen/add flares over, etc… Depends on the shot…
What do you like to do?
I try and match the Flare. Rebuild it in action and then add that back on over the top.
I have just done a couple of CG muzzle shots with heaps of lens flare like this.
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I stabilise around a point with little detail, freeze a frame without the lens flare, subtract this (no clamping!) and blur the result (if needed). Now this get’s added over the element, that shall be integrated. Using this you get the animation for free. Works best on lens flares that don’t have much detail.
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I lift the flare, get a broom then sweep what I’m trying to hide under the flare then drop the flare back down in place hoping it doesn’t get noticed.
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That’s a fantastic metaphor for a lot of things we do… 
On the ‘Pirates’ films, John Knoll would rent the lens, and shoot the flare that was needed on black using a DSLR with a PL mount in his garage. He won an Oscar.
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And Knoll Light Factory v1 was born!
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This was long after Knoll Light Factory was written, but I believe the rig in his garage was the same one he used for studying flares for that tool. Funny to hear the author of that great software say it was sometimes easier just to shoot it.
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Fascinating Sam. Amazing what great things come from garages… WFH FTW… 
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Knoll Light Factory was my go to Flare tool for years… at some point it hadn’t been updated in years, i think it only worked in 8 or 10bit which is around the time i ditched it but looks like Red Giant is keeping it alive. Amazing this tool is still being sold…
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I can’t tell you the number of times @ Imaginary Forces that we would take a camera into the bathroom w/ black duvatine & lights to make flares/flashes/leaks for a title sequence. Refraction objects, celluloid, prints on acetate, whatever we thought might look cool. I think at the time we had a Canon XL1, a DVX100, and then several years later the HVX-200 came out. Those were fun times…
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