Hi heartandmind
Well, you're not alone with feeling guilty about how things go regarding separation, that's for sure!

Based on what you've shared, I'd like to offer you some hope and encouragement.
... .only to contact me back once the following day and disappear again.
As you could imagine, these behaviors leave me feeling very hurt and, ironically enough, abandoned myself.
I can see roughly how this can follow, and I do think it makes sense--but could you embellish more on why you felt very hurt and abandoned? These are quite strong feelings to have based on the history of your situation that you've described.
Well, I didn't really even understand what that response particularly meant and felt that it was rather cheap after my very long and emotionally feeling inquiry to her. Due to this, I did not respond.
I'm not saying a lack of response is wrong--I'm just curious as to why you chose not to respond. I do think that sometimes not responding to certain things can be a good idea.
Two months later, I feel very guilty. ... .The reality is, I will always, always, always be here for her and really am struggling with even the concept of her thinking that I no longer may be after this.
^ this can be a great focal point for you.
Though I am happy that I set a boundary and stood my ground, it leaves me terribly worried that she will push back even more and maybe this time for good. It is also possible that I am overthinking this (I definitely tend to!)
Well done on setting that boundary and standing your ground. Boundaries were one of the hardest for me to enforce.
I think this boundary is hard for both your partner and you. Many boundaries seemed to feel this way for me.
I think with new boundaries, you'll always feel that uncertainty of whether what you're doing is right or wrong. It's a new thing, so feeling uncertain is normal. It breaks a pattern that worked for you in the past, so there's even more uncertainty. You may have a highly reactive partner, so that's even more uncertainty. It helps to really notice that this uncertainty is expected. Know that it's sometimes a natural product of setting limits.