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Hello I am Dr RB and I am a small animal veterinarian. German Shephards are very astute and intuitive dogs.. What was Charlie and Ivy-Anne's relationship before this? Were they very bonded or did that just tolerate each other. My initial thought is that she either did something to him to really tick him off OR she had some kind of instance (e.g. tremor, seizure, abnormal behavior) that he is trying to alert you to. Has she been having any abnormal symptoms?
If not, this may just be a strictly behavioral issue. I would continue to separate them in shorter intervals to see if the barking subsides. I wouldn't associate any negative trigger to this such as spraying the water/vinegar. If this continues, I would call your regular DVM and request he/she prescribe a mild sedative for Charlie to help you and continue with the separation intervals while he is more relaxed.
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