Drol, ive taken the same aproach (using win lirc and transfer to the phone) some time ago (except for needing sometimes to record the ir signal a few times) it works ok, a few point to take in mind:
-the file generated wil go to the "device" forlder, not the "remote" folder. The remote folder basicaly is the folder for the file generated by qtirreco, it states wich buttons, color, order etc, then it redirects each button to the proper device and command from the device folder (you can have one remote with several devices linked). You have to generate the remote control inside the qtirreco program and the generate the buttons etc selecting the device you generated with winlirc.
-there are some remotes you wont be able to record because the need of a feedback, ex the ac, usually the ac has an ir receiver and transmitter, and signal is exchanged between the remote control and the ac unit, you cant emulate this with the n900 because it wont respond to the ac when it recieves a signal from it, all my other devices work ok, tv, home theatre etc, its preatty easy once you get it working
anyway im here if you need help getting this to work,