Actually, that gave me an idea. Since only some shapes stopped accepting connections, simply creating a new shape (in my case, a rectangle) and transferring all the connectors to that shape worked. Then, delete the old shape. Don't copy the old shape, as you'll probably be copying the same problems.
This happens to me as well. My diagram has over 1800 shapes on it on several layers, the majority of them being connectors. Some shapes (rectangles) won't accept any connectors any more. Copying the diagram to another document is not an option due to its size.
All you did was remove the primary key constraint, not the unique identifier. If you don't want it to appear under Unique Identifier in the Repository Object Navigator (RON), you have to delete the UID from your Edit Entity screen (or directly in the RON).
If you were to generate your server...
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