Thank you Nita. You have helped no end.
I'm a bit embarrassed now. I had forgotten about RoboHelp HTML (in my defence I haven't used RoboHelp in almost three years).
Converting the HDK source Help file to RoboHelp HTML created a useable source which could be converted to Flare without further work because RH X5 created an .xpj - although I might still generate the webhelp and pick up the .hhp file to see if it makes things any better, but that'll have to wait for another day as the project is over 6,000 topics and the compile and conversion times are correspondingly longer.
The conversion from HDK to RoboHelp has lost the index entries and map IDs from the original help (it had no toc). I'm not sure map IDs can be converted as they were handled very differently in HDK (I seem to remember problems around this when we converted other projects to RoboHelp in the last century), but I'm going to see if I can convert the index entries. It has, however, converted the old HDK hyperlinks (which were hardcoded in HDK) which is the one thing I really wanted to convert. I don't mind building a new index and alias file, but manually recreating tens of thousands of hyperlinks would have made the conversion impossible.
The style information hasn't come across intact either, with some of the styles having the wrong font size or losing some settings, but that is pretty easy to fix in the style sheet.
I'm going to play around with the conversion to RoboHelp to see what, if anything, I can salvage there before making my final conversion, but it is looking more promising.