I was having the same issue by using an IF statement to return an unwanted value to “”, and the chart would do as you described.
However, when I used #N/A instead of "" (important, note that it’s without the quotation marks as in #N/A and not "#N/A"), the chart ignored the invalid data. I even tried putting in an invalid FALSE statement and it worked the same, the only difference was #NAME? returned as the error in the cell instead of #N/A. I will use a made up IF statement to show you what I mean:
=IF(A1>A2,A3,"")
---> Returned "" into cell when statement is FALSE and plotted on chart
(this is unwanted as you described)
=IF(A1>A2,A3,"#N/A")
---> Returned #N/A as text when statement is FALSE and plotted on chart
(this is also unwanted as you described)
=IF(A1>A2,A3,#N/A)
---> Returned #N/A as Error when statement is FALSE and does not plot on chart (Ideal)
=IF(A1>A2,A3,a)
---> Returned #NAME? as Error when statement is FALSE and does not plot on chart
(Ideal, and this is because any letter without quotations is not a valid statement)