If both are lectures, you should be fine. I was in the same situation last year. Skip two lectures of one course and one lecture of the other each week, it shouldn't be too bad.
There's two criteria I explicitly came up with to decide on which lecture I'd skip:
If you want to take both courses (i.e. you're interested in at least one of the subjects) then skip the one you enjoy more, so you'll enjoy catching up on your own time. I didn't do this myself, but it seems like good advice.
Personally, I find example-based lectures to be a waste of time (mostly), so I skipped the course that was example-based and attended the lectures for the more theoretical course. This directly contradicted my first criterion, though, which is why I didn't follow it...
That's why I used 'came up with' above. I didn't actually apply both criteria, although I think they'd be pretty useful if applied.
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