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If I understand your question correctly, A and B will NOT be selected (the rename has no effect for the originally unselected fields)
You can see this by setting up a flow that just consists of an input (e.g. Excel), a select set up as you described and a browse. If you set up the input to use a sheet with just the 4 fields, the output will be fields B and D. If you reset the input to a sheet with additional fields (E and F) the output will be B, D, E, and F
The answer varies SOMEWHAT by tool - but see my final sentence.
For example, the select tool will not output A and C in your example, because you told it "fields named A and C shouldn't pass".
The multi-field tool is a longer story. A and C will not get TREATED by the formula, because you told it "fields A and C shouldn't get treated by this formula". So - New_A and New_C will NOT be in the output; but if A and C were in the input to the multi-field tool, A and C WILL come out; because this tool is ONLY saying "apply this formula to these fields" and you are excluding A and C from those fields.
I think the general answer you're looking for to your question is no - A and C, if present and unchecked, won't get treated along with other fields in the various tools that use dynamic / unknown inputs.