Even the presence of flame arrester may not be sufficient. Checking through some of the literature, I found a reference to where a fuel/air mixture was “spontaneously ignited by a hot spot directly opposite a lightning strike to a [aircraft] fuel tank” (Bragg 1968). Bit of an old reference, and I am sure fuel tank design has moved on since then. However, it does suggest that caution may still be the prudent course of action. Creating a fuel/air mixture, even though venting, does seem to be taking the risk of encouraging a lightning induced flame.
Another possibility is intercepting the lightning stroke corona by way of a corona shield on pipes venting a fuel/air mixture. This is normal practice for the fixed, permanently venting, vents at chemical plants and such like. Is there a similar corona shield arrangement on the vents from aircraft fuel tanks? If so, then I imagine it is theoretically safe to continue fuelling if the connection into the tank is vapour tight. ‘Theoretically’ is the key word here, as I, from a personal point of view, would not feel comfortable putting the theory to the test!