>When a table is added to a DBC it is linked with a unique id. One cannot overwrite an old table with a new one by the same name because the ids won't match and the DBC will complain.
>Question: What is the best method to update an EXE of an previously installed app without overwriting the old data tables (hence, the data)?

I put my non-data application files in a subdirectory of my development tree called "PROD" (production). I then create my setup files starting in this directory. This prevents any inclusion of data files. I can also mimick my application tree under this subdirectory if needed.