When i create new Folder/template in Templates PLSQLDeveloper "clearing" all my remapped keys. Keys are mapped, but not working. Some keys are worked fine.

When i open "Key configuration" dialog and click "Ok" then all my remapped keys work again.

I cannot reproduce this. Can you let me know the exact steps?

Yes of course.
Example:
1. Open Tools -> Preferenses -> Key configuration and assign "ctrl-D" key to "Object: Describe" item. Close form by click "Ok".
Try to use this key to any objects (my case is table object), rigth mouse click to table and you can see what key "ctrl-D" assigned to "Describe" action.
2. Open templates tree and create new folder "MyCollection" (or create new template). Try to use "ctrl-D" key and you can see what assigned action not work. Rigth mouse click to table and you can see what any keys assigned to object actions was cleared. You can't use they.
3. Open Tools -> Preferenses -> Key configuration again and you can see what key are still assigned. Close form by "Ok" button and all keys assigned to object actions now work again.

This does indeed not work correctly. I tested this with another function, so apparently this applies to specific function keys.

We'll fix it.