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I removed an assembly not needed in my master assembly and it is still showing as a parent. This sub-assembly was deleted from the system. I can I remove this parent from my master assembly?
Try switching from References view to Dependencies view (the option rigth under Reference Filters tab). Then check if next to line connecting your model to missing parent is small (like very small) recycle bin icon. If it's there click it to break dependency between your model and missing master and save the model.
Sometimes if your 1st part in the assembly is installed as "rigid", it locks it. Try moving a part before it and then deleting it.