There is the following line in the cfcompile.bat file of CF 10
set CFUSION_HOME=%~dp0%\..
I let it be. In fact, I use the default file that ships with CF 10.
To recreate your scenario, I copied some CFM files to the directory C:\ColdFusion10\cfusion\wwwroot\filesToCompile. I then ran the DOS command
cfcompile -deploy C:\ColdFusion10\cfusion\wwwroot C:\ColdFusion10\cfusion\wwwroot\filesToCompile C:\ColdFusion10\cfusion\wwwroot\filesCompiled
I browsed the CFM files in filesToCompile, comparing each to the corresponding file in filesCompared. There was no change, as expected.
There is perhaps something not quite right with your original CFML code. Could you show it to us.