Oh, I was TOTALLY like that, and I do think it is at least somewhat an Aspie thing. Or a female aspie thing. Or an insecure aspie thing.
The thing is, I feel this sense of dread and anxiety
whenever someone leaves. If I actually like them, anyway. But with friends, I know that running after them screaming "DON'T GO!" is just crazy. It just takes me awhile to calm down after they go. It's the change and uncertainty that get me. Once I can get back to routine, it's fine, but in that moment, there is nothing that can make it fine because they are going and that has disrupted everything. (That sentence is what happened when I tried to articulate the feeling. All-or-nothing thinking, much?)
For some reason, with significant others, I don't have the same block. Maybe it's because the intimacy has led me to feel that I can cross boundaries I can't with a friend and expose them to my meltdowns. Maybe it's that the feeling is that much more intense, and I really CAN'T control it the way I can with friends. Probably both.
The most I can say is plan out transitions, make sure she knows what she's going to do when you leave and that it's something she's happy with, make sure you leave exactly on schedule and she knows when you will come back, and keep contact while you are gone to remind her that even though you have disappeared, you do in fact still exist and care for her. This may seem silly. But it helps. Of course, everyone is different and these are just one person's suggestions.
It's harder than prepping for other kinds of changes for the reasons Judge mentioned above: not only is this a change (which in itself is difficult for aspies), she is also emotionally sensitive, and she relies on you to cope with the world (for me, it's executive functioning as much as or even more than social things). So this is like a triple whammy. And yet, because it's so normal for other people, it feels all the more ridiculous and guilt-inducing when it happens.
I recently revisited
this list of female aspie traits and was reminded how great she is at describing women on the spectrum. So perhaps you can find more there (I was looking for something specific but I forgot!). I must say, it's wonderful that you try so hard to understand your partner and her triggers. Really.