"I guess you've known this" is in the wrong tense. It should be "I guess you know this". Your boss's word use is strange but I agree that you shouldn't say it. When people say things like this, it sounds passive-aggressive to me.

I agree with your boss that it creates alienation. Some people may view it as a "passive aggressive" statement.

There seem to be different opinions on this in the comments, and I’d say they are all correct. The meaning of the communication depends on the context — who the reader is, what your relationship is, what has gone on before. I'd say we can identify three mistakes that we can fix in order to improve your future communications. The way you put it, it seems you are assuming they already know something, but if they already know it, then why are you telling them? That's your second mistake. Your first mistake was making an assumption as to what other people know. On the other hand, it is understandable that you don’t want to risk underestimating their prior knowledge. You have a tough job, and many native English speakers would have trouble choosing the right verbal tense, aspect and mood (your third mistake). Here’s an idea (again, depending on the entire context of the on-going relationship): You might write something like, “as you may already know”. The modal verb “may” shows that you’re not making any assumptions as to whether or not they already have the information, so you’re offering it just to be thorough and conscientious, while at the same time recognizing that you cannot read their minds. The adverb “already” suggests that if they don’t yet know, it is perfectly normal (so there is nothing to be ashamed of). If you have additional questions or comments, go right ahead and ask me.

No, I would not say this sentence brings on a sense of alienation. For that you should read some Sartre! I suspect your boss would prefer a formulation such as ‘as we both know’ which is more inclusive.

That's actually the opposite; it subtly conveys that you regard the reader as intelligent enough to know what you're talking about. Had you said 'I guess you don't know this', you'd have appeared rude. The only thing you should change is that it should say 'I guess you know this' or 'I'm sure you know this'. 'I guess you've known this' implies they don't know it anymore, and also sounds a tad strange grammatically (not incorrect, but unusual). 祝你好运。