I use CDEx from a thumb drive, bringing it whereever I need it. I also use the FLAC external encoder. This raises problems in CDEx when the drive configuration changes, as CDEx uses an absolute pathname for the external encoder. Thus, when my thumb drive goes from F: to G:, the FLAC encoder can't be found.
Unfortunately, there is no way in CDEx to reference the FLAC location without the full path.
The suggestion (if this project is in fact still alive, that is) is to change the preferences window to use the simplest path to an external encoder. Thus, if FLAC is in a folder named FLAC beneath CDEx, store just "FLAC\flac.exe". This would allow portable installations to work regardless of the base machine.
The advice is a workaround: it is possible to edit the CDEx.ini file and change the setting there, and have it work as I suggest above. The ini file has an entry STRUSER1 that stores this path, and removing the drive designation doesn't appear to affect functionality.