this note has sat there with no response....so i thought i would give this my best shot on how i would handle it.....though i can't claim i have dealt with this exact issue.....but a couple similar ones.

first, my view is don't think about 'staining' or 'tinting it' it.  while epoxy soaked flour may be stainable to some degree...i think you would spend a lot of time and effort for an uncertain result .  stain introduces a 3rd color to the mix and i think you will find it challenging given the substrate and the fact that there is no tint that really matches the other wood flour you are trying to match.

if you want to get it to match, my first thought would be acquiring more wood flour of the same color you did the other fillets in.  clc may be the best source.  overall, i find they are pretty consistent in their wood flour color.  

i would then sand the existing fillet (try to take it down a millimeter or two with 60 grit sandpaper), next, i would then paint the fillet with clear epoxy.  i would then sprinkle the 'correct color' wood flour over it so that it is covered.   when it has cured a little bit.  i would blow off the excess wood flour and paint a final coat of epoxy over the wood flour completely sealing it.  the idea is to get a complete 1 to 2 milmeter or so covering of the old fillet with a color-matched fillet while keeping the size the same. 

since the under-fillet is a light color, i think this should work well, this technique will act like 'painting' a color matched fillet over the old fillet.

that said, it's hard to tell without pictures just how noticable this really is.   as the builder, its easy get caught up with little mistakes.  i am currently working on a build of a strip-built where i got distracted while working with my ros sander and created a divot in the side of the boat i am building.  i 'patched' it by creating 'matched' veneers with scrap strips, gluing them over the depression and refairing it.  to me 'the fix' is clear as day.  two friends walked the boat the other day and nobody noticed a thing.  i am going to go with it and get on with getting my boat on the water. 

best of luck,

howard

You can tint epoxy with a powder-based stain (aniline, Mohawk, etc.) or a small (less than 10%) amount of UTC-type pigment, and just brush a thin coat on top.

Or, gently sand the fillet, and stain it directly, using the sanded texture to hold the stain. Let it dry, (check to see how it looks), then gently brush a thin clear coat on top. Most stains will dissolve a little here, so don't move the epoxy around, and don't let it run/sag. Experiment first...