Some epoxies are blush free and if in doubt, you can contact your epoxy manufacturer. they will tell you how long the window of opportunity for re-coating is. Generally, it's always best to re-coat during the early stage when you get a chemical bond. I re-coat asap as soon the epoxy is dry to the touch (usually overnight).

Ideally, you ant to fill the weave fully. You will sand anyhow before the varnish coat. If some glass gets exposed (which it will) it will still wet out perfectly if you sand with a very fine grit. I usually wet sand with 400 or finer. If you still see some areas where the weave pattern is visibly, you could wet sand it fine and it will wet out fine. Don't forget, you are often looking at epoxy on top of fibers and not the fibers themselves. I usually don't skimp on my fill coats because I learned through experience that it makes life easier in the end. You can also just add a little more fill to one area with a brush.

If yo go on vacation, wash the shiny epoxy with a stiff brush or a scotch bright pad and water before re-coating.