From my brief experience (I have no device yet, just the Windows simulator), it looks like the pdc.exe utility on Windows is not overwriting any *.pdx files when using the same output directory repeatedly. I can make a change to my main.lua file, run the compiler command (PowerShell: .\pdc.exe <main.lua location> <output.pdx>), and it will overwrite the pdxinfo file, but nothing else. I have the CoreLibs folder copied in my source, so it replicates the lua->pdx files too, but those *.pdx files remain the same timestamps between rebuilds as well.
Temporary workaround is just to kill that <output.pdx> directory before your build process. I have not had any time to work up any complex build scripts, as this is just my first 30 minutes trying to develop something.