are you sure your compileing MDL into the correct format (ie check your settings to be sure the export settings are set the way they were when it was working)
are you using the CORRECT exporter? IE if you got one for FSX and another for FS9 are you using the FS9 exporter (to my knowledge the FSX SDK comes with its own IIRC)
check the file its self, are you moving the correct file to the proper location and completely closing FS9? If FS9 (or any flight sim for that matter) is running you change the file, the changes will happen, however you WILL NOT see the changes untill one of two conditions have been met.
Condition 1: you compleatly and utterly kill the FS9/FSX process(es), and allow FS9/FSX to reload its self there by allowing the program to relaod the new info
Condition 2: (this is while running FS9/FSX and also assumes your currently in FREE FLIGHT mode) go to your aircraft menu pick a new aircraft (one that is DIFFERENT, IE if your working on a cessna 172RG select somthing like a boeing or other manufacture, but NOT another variant of the 172RG) and then let the plane load (hit select as if your going to fly that new selected plane so your back in the flight deck view of your new plane (selected one)
then go to the select aircraft menu and select the plane your working on/just updated
NOTE: Condition 2 works for me just find when working on textures, and should still work in regards of the model, but always make sure you keep back ups of your plane in a safe location! I will leave it up to you as to what methoud you want to use but I hope this helps you out some how...if not I hope you can at least get an idea of where to start the trouble shooting process...