When I asked my doc about using Aquaphor, she didn't seem to be terribly adamant in either direction saying that since the application is on over night, a topical ointment the next day "probably" won't interfere with the effectiveness of the Carac.
I decided to try Aquaphor after reading other postings, particularly the ones from Luckycat (Side Effects of Carac or Efudex - 200 postings) about her success using vaseline (first mentioned on page 2, 4th posting scrolling down). She continues her postings throughout the process including the week or two after when she reports wonderful results.
Sooo...on day nine I'm looking pretty bad, but keep in mind I'm doing all around my lips, too. Also, I have had two biopsies showing multiple AK's. BTW, thank your doc for not cutting into your lip as a first option. As I mentioned, I let it go too long and then took the laser route (vanity). The biopsy site on my bottom lip may require a graft...yuk!!
Bottom line: If it was me (oh, actually it is), I would use a soothing ointment, if the alternative is stopping the treatment all together. Also, I think your doc is right, the site reaction to the Carac will tell you if you need to continue. If so, it will NOT resolve itself.
Let me know how you're doing.
Carole