There are several major issues (IMOs) in this approach:
EF, like any ORM, relates to the issue of persistence. Thus, this should not interfere with how you structure your domain model. The fact that all of your entities are stored in what sounds like one store of preservation may be a sign that your limited contexts overlap or are missing.
Trying to move to a better structure is not bad :) --- however, as Mark Oreta stated, I probably would not have bothered with the structure of EF.
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