I faced a similar issue where the Series drops down to Zero.
I have a Pivot Chart linked to a Pivot Table with multiple Series for 7 different Key Figures & other Fields. I pick up my source data from BEx/BI using Formula to bring in some extra Columns & apply some miscellaneous formatting. This data is then forms the basis for my Pivot Table & Pivot Chart.
I found that you cannot filter the Pivot Table as the Fields do not contain items. You cannot use NA() or even "" (double-quotes) using Formula - this is because when using different kinds of aggregation within the Pivot Table the NA() cannot be SUMMED and hence the Series is not displayed. It also appears that setting a Cell to blank using "" (double-quotes) in a Formula has no effect either. I even tried #DIV/0! errors & then hiding the errors - no luck.
As a workaround, the "only" way I have found so far that works is to manually Filter my final data input for the Pivot Table by zero and then simply delete the values. Refreshing the Pivot Table then allows the Pivot Chart to hide the blanks and the data points will not be displayed. This means that any Series with intermittent values are displayed correctly.