Based on duo work with recorder players, I'd second andante's suggestion of Bärenreiter - the realisations are significantly more tasteful than those which seem to be an exercise in drowning out the other player.
The other consideration you'll need to make is that a good realisation for harpsichord is not necessarily a good realisation for piano, and it may be the case that the score from which you are working was aimed for the former rather than the latter. For instance, if there are runs that mirror the flautist's part, this doesn't always work as well on piano - in this case, try only playing the notes on the beat; or the half beat; or the first and last note of each triplet/semiquaver group. Or, if there's a chord that is repeated for no particularly good reason, and the accumulation of sound is problematic, skip some of the repetitions. Granted, this does require some 'reworking', though it need not be on the fly (cross notes out with a pencil), and in any case, missing notes out rarely makes the accompaniment harder.
Finally, a good source to look at for hints on accompanying is Quantz's 'On Playing the Flute'. As the title suggests, it's most commonly used as a source of advice for flautists/blockflötists, but it discusses the task of accompanying, too. (Indeed, the suggestion above of only playing the first and last note of a group of semis is a suggestion for 'cellists when faced with arpeggiated semiquaver passages that only make sense on keyboard.) It's likely that your flautist friend has a copy, or if not, they need one

.