You may leave both of the catalogs to co-exst and use the Catalog name overwriting to let the generated code targets the new catalog for all entities previously generated to use the old catalog.
Refer to the LLBLGen Pro manual: "Using the generated code -> Application configuration through .config files" to
And if you want you may remove the old catalog with all its entities and re-add them from the new catalog.
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You may also check the newly released "Project Converter", you can find it under v.2 downloads.