Merging a data-file with a UI-file into one

Since from the beginning of my ERP solution with 20 tables I kept
according to the data separation model one file with the UI and one
file with data. As I developed the solution further, however, I was
forced to add calculations and relationships into the data file, which
made things quide complex.
Because of this I now want to merge both the files into a single one,
but I encountered a problem. As I imported the tables into the UI
file, filled them with data, in the relationships graph the tables
showed with a trailing number (original "table", after the import
there was also a "table 2" box). To preserve all the relationships in
the UI, I then pointed the tables in the graph to get data from the
imported tables. However, when I then wanted to remove the imported
"table 2" from the graph, all the layouts lost their link with the
proper table. If I wanted to get them work, I guess I should have left
the imported "table 2" in place and redone all the relationships...
Anyway, anyone would have some comment or experience to share?
Thanks a lot! Jan