As of Darcs 2.10.2, it is not possible to mark conflicts only in a given
file/a list of given files. That is, mark-conflicts always trashes all
changes in all files of the working copy.

I have a working patch for this (tested in simple scenarios). Could be
ready for 2.12.

As usual I got side-tracked by trying to implement something much
better. Instead of just limiting the destruction to the files given on
the command line, why not try to /merge/ the markup with the working
tree? But this needs to be a special merge, one that /refuses/ to add
new conflicts and instead offers the user a choice to (a) keep the
working tree version, discarding the markup that conflicts with the
user's changes, or (b) replace the user's changes with the markup
(defaulting to (a) as the less destructive choice). The choice should be
offered on a per-hunk basis and only when necessary, automatically
keeping as much of the user's changes as possible.

Well, as you want, but maybe a patch that just brings the mark-conflict
behaviour to a per-file granularity is good to have for the moment.