Ugh! That stinks!
I've occasionally had magazine poems published with text changes I didn't approve. Usually, I'm fine with it and they're quite minor. But a couple of times it was upsetting because the meter got messed up. It's MY name on the poem, so I feel it makes me look bad when the meter is off.
If I were you, I'd write a polite note to the editor. Especially if you're a regular contributor. That's what I did. I complimented the illustration and the magazine in general, but mentioned that I was slightly upset about the edit (I forget how I phrased it. I think I said "concerned".) and asked them to please let me know next time (if at all possible) so that I could help them think of solutions for any problems they might have. I so appreciate it when they ask first! They usually do. And I'm more than happy to provide them with options.
But leaving off an entire line? Of a limerick, no less? Wow. I'd be pretty livid. Could it have been an error?
If they don't give you some sort of reason and apologize, I don't think you should sub there again.