I'm guessing that the main parameters are re-loaded but not the PLC program,and that it was running from ram rather than the eprom. There will be a parameter that chooses between running from eprom or ram (its 77 on my TNC355 but will be something else on your machine).
Running from ram is normally only used when developing the machine implementation as it can be edited 'on the fly', then written to the eprom. Depending what stage your machine was at in the developemet cycle you may get lucky and have workable code in the eprom that you can run.
Andrew Mawson
East Sussex, UK