Hi,
seems that define always looks in the standard library for the EHT data, even if you take the basis sets from your own library. Only the basis sets themselves are read in from the settings in ~/.definerc. Usually sufficient since the EHT data does not depend on the basis set, but this is of course different if you have ECPs with a different number of electrons in the core...
If the problem is that you are not allowed (or do not want) to change the default files of the Turbomole installation, a simply trick would be to create your own TURBOMOLE directory and add symbolic links for all directories to the 'official' Turbomole installation, except 'basen'. Copy basen and change them in your local directory. If you then set $TURBODIR to this pseudo-installation, it should work (although I did not test it). If disk size is sufficiently large, why not copy the whole $TURBODIR directory to your $HOME ?
Regards,
Uwe