It's so hard to leave them, especially when their still puppies, but I think eventually they get used to it. I would also leave a tv or radio on for him, so there's some sort of noise. Are you shutting the bathroom door or leaving a gate? I think a gate would be easier for him then shutting the door.
Don't worry about being emotional, it's perfectly normal!! When I was on vacation last week I couldn't think about my two or tears would start coming. And I hate leaving them while I go to work/school as well, just something you gotta do though.
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