What Walaa reproduced is below and this is expected:
I have created a simple database with 2 tables. (Category and Product)
Each with 2 identical fields (Id & Name), without any relations.
I created a project in LLBLGen v.4.1, and had both tables in the catalog explorer, but only mapped Product as an entity.
Then went to the database and renamed the product table to ProductX.
Refreshed the catalog, and picked ProductX table (so Category and productx are now selected)
After refreshing, The Product Entity in the project Explorer got mapped to the Category table.
So I guess it picked the first entity it found having the same fields.
This happens because after the refresh the original target of Product isn't found (as it's been renamed). So the engine then tries to find the table back, as it might be renamed (it was). However it doesn't know what the new name is, so it tries to find a table with the same fields as the original. In Walaa's example above, Category is the first table it finds which has the matching fields and which wasn't mapped as an entity before, so it could be the table with the same name, so it picks that one.
I have NO idea if this is the same situation as you run into, because:
In the database I rename a table.
In the designer I refresh relational model data from a database
In the list of tables I see the new table, but not selected.
that last sentence: what do you mean with 'list of tables' ? The list of tables shown during refresh? I am a bit lost what exactly you want to achieve and what steps you take and which give different results than you expect.
So please post precise steps what you do and what you do expect what should happen and what actually happens.