what I described is the easiest option - otherwise, you would need to review/modify the C++ code to come up wit a converter tool from scratch.
If you have several files, possibly with hours of data, you could automate the loading/saving using Nasal scripting and a handful of fgcommands to load other CSV files, and control the flight recorder subsystem accordingly - in fact, you could even append CSV to the same fgtape that way.
If the 32x speed-up is working properly, you could remove the hard-coded restriction to see if your system can speeding up beyond that. If it does not, you can use the minimal startup profile on the wiki to disable most systems (including rendering using draw masks) to reduce the load on the simulator.
But it's s a pain/gain thing obviously, because you may have to touch C++ code and rebuild fgfs.
Personally, I would rather do that than come up with a custom conversion tool - i.e. it is much easier to modify a few hard-coded constants/variables and then use fgfs "as is", than coming up with a tool from scratch.
I guess it would be a good idea to tell us exactly how many hours of flight data you have, and what you are hoping to do with it - and if you are able to rebuild fgfs, and know C++ ?
With a little Nasal scripting (probably not more than 50 lines), you could certainly automate most of the task at hand.
I could tell you exactly how to write a CSV->fgtape conversion tool in C++, i.e. by reusing portions of FlightGear's C++ code, but I don't consider that effective - it would be much better to remove hard-coded restrictions that prevent FlightGear from being used for that purpose.
To disable rendering, see:
http://wiki.flightgear.org/Draw_masksThere also is a switch/property to disable scenery loading, too.
For the property names related to sim-speed-up, see $FG_ROOT/gui/dialogs/timeofday.xml
You will find that it is using /sim/speed-up
and that it is using $FG_ROOT/Nasal/controls.nas (see line 506)
Which is also where the factor 32 is hard-coded
I would suggest to change that, or make it configurable, and then disable other features like rendering, and then use the minimal startup profile that you can find on the wiki, you will probably want to customize that by adding the draw-masks, and removing the location/offset stuff at the beginning:
http://wiki.flightgear.org/Template:Startup_ProfileIt will look really bare and simple, but will provide much better performance, which you can use to speed-up the main-loop accordingly