How should I handle toggling of chart series based on groups of checkboxes?

I'm modifying an interface for an interactive line chart that can contain anywhere from one to twelve series of data. Users will be able to choose which series they can view by clicking on a set of checkboxes.

The checkboxes are sorted by type of series; three checkboxes per series, as well as a "show all" checkbox that will plot all of the lines in that series. There is an additional set of three optional checkboxes at the bottom that allow the users to cut "across" the data to see date-specific, rather than series-specific, comparisons.

Here's my question: how should I handle toggling of the "show all" checkboxes?

Currently, if a user chooses either a "show all" checkbox or a date-specific checkbox, all of the chart's existing lines are cleared and new lines are drawn based on the boxes chosen. My thought here is that this behavior would prevent cluttering or "muddying" of the data.

What I'm concerned about is whether that's a bad experience for the user. Say I chose a checkbox from each of two different series, and then chose a "show all" checkbox from a third series. Would it be confusing to see my first two choices removed?

I'm including an edited screenshot of the interface, which is still currently in the review stage. I would greatly appreciate some sound guidance. Thank you!