(Refer to the 'mark the text wrap float "broken"' for why.)
Wrapfig seems to work better than floatflt, at least wrapfig outputs the figure in a case where floatflt silently looses it. It is easy enough to make a patch that simply replaces floatflt with wrapfig, by changing the \usepackage as well as the \begin -- \end commands that LyX outputs. Would that be an acceptable starting point? I think this can be done without changing the file format, as wrapfig seems to support all the floatflt options. Now wrapfig supports some more options as well, supporting those will need a format change as well. Helge Hafting