Some more details about your data would be helpful to answer that question. The answer is likely no, but it's hard to say for sure. What does your data, in both indices, look like? I'd primarily like to know the fields you care about from each one, as well as what each document in each index represents.
The short answer is, if you can't condense both sets down into the same number of rows that both share a value in a shared column (this would allow joining the data), it can't be done.
If the schema of the data is the same, you can certainly query both from Elasticsearch and mix them together that way. I'm guessing since you asked (and based on what you've said is in the data) this isn't the case.
You could make two different elements, one for each index, and simply overlap the two, but that only works if you always have data. If the data is sparse (ie. some chunk of time has no results) and that is at the beginning or end of the data you are visualizing, the axes will be different and the overlapping charts won't show the same ranges.
In a more general sense, the visualizations in Canvas today all work with 2D data, columns and rows, like in a spreadsheet. You'll need to be able arrange your data (at query time or by chaining functions in the expression) into that shape in order to visualize it in a single element. At a minimum, you'd need the same number of rows, and a 1 to 1 relationship, from the results of both indices. We don't currently have a way to "join" data in the expression, so you'd also need to get everything from both indices at query time. Which, again, based on what you've said so far, I think is not your case, but more info might show otherwise.