Whenever you delete an element from a diagram using the Del key or by using the context menu and selecting Delete, Enterprise Architect will only delete the Diagram Object for this element. The model element itself will not be removed from your model, so Embedded Engineer will still generate code for these elements.
You can easily locate such elements by using the so called Find Orphans search in Enterprise Architect. Select Edit → Search in Model (CTRL + ALT + A). In the first Combobox, select Diagram Searches. In the second, you can now select the function Find Orphans. Execute the search - the listed elements aren't part of any diagrams in your Model.
Orphans are not always a problem, but it's not very common to have elements without them being on a single diagram. Don't just delete the elements without further examination.
To locate these orphans in your project browser, select Find in Project Browser from the context menu in the Find Orphans search. You can also use the Traceability view in Enterprise Architect to further examine the orphans and to decide what to do with them.