I just had another quick look at this myself.
gerbv can load an Excellon drill file and export it as a Gerber file.
The Gerber can then be opened in a text editor and all the aperture sizes and references removed apart from one which is set at the required size, say, 0.15mm or so. This file should then hopefully load into Flatcam.
It is all a bit of a faff because this would mean doing two passes over the board with one for the traces and another for the holes but it is worth an experiment.
An example, if the formatting is not all over the place
G04 This is an RS-274x file exported by *
G04 gerbv version 2.6.1 *
G04 More information is available about gerbv at *
G04 htt://gerbv.geda-project.org/ *
G04 --End of header info–*
G04 --Define apertures–*
G04 --Start main section–*
Edit: Well done bobc, you posted while I was still trying to get my post to format properly,
That is the difference between someone that knows how to code and someone that fudges around problems