It takes time for your emotions to catch up to logic. The important thing is to keep reminding yourself of the logical thing to do. You may have some hiccups but with hard mental work you will eventually get your emotions to catch up with your logic.
This is ABOSLUTELY TRUE - a relationship with a person with BPD can, and often will, impact your nervous system. I'd say it took me about a year before the two started to mesh again. Now in my case, she abused me pretty badly - so for every one it's different.
Hero is right, there are hiccups. Some people may trigger you without you even realizing it. So don't neglect what your body is telling you. It may just be telling you that it needs to rest a while to heal.
No shame in that.
Hang in there.
Rev