This answer does not fully deal with the OP, but there are have been several times I have had a similar problem and searched for the answer.
If you can recreate the formula or the data if needed (and from your description it looks as if you can), then when you are ready to run the portion that requires the blank cells to be actually empty, then you can select the region and run the following vba macro.
Sub clearBlanks()
Dim r As Range
For Each r In Selection.Cells
If Len(r.Text) = 0 Then
r.Clear
End If
Next r
End Sub
this will wipe out off of the contents of any cell which is currently showing ""
or has only a formula