Hi Chris.
I have just done the similar repair to a Hillman Minx Estate wagon, The inner panel are flanged on the guards which are fully welded to the body. Epoxy is not good for that area if you are hammering down the flange as it cracks, I used Anchor Wax on the seams and will treat it further with wax again once the car is painted, I wouldn't use any sealer on flanges unless completely covered as Neil mentioned.
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John
EK Holden V8
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