Conventional wisdom is that you should smoke your pipe down to the last shed of tobacco. This will normally mean a few relights near the bottom and this is no bad or shameful thing. However, I have restored a lot (probably getting on for 400) of estate pipes and many, if not most, show evidence that the previous rule is actually the exception. In all cases trimming back the cake has restored the pipe to "useful" condition (and they were quite obviously also useful as they were to the previous owners). I haven't had any problems with inconsistent use of the whole bowl of the pipe causing cracks, burns or anything else sinister. They may smoke better if the cake extended further (it can't really build consistently - the draw hole would be obscured), but again I don't believe that any real damage will be done.
My advice is:
Don't sweat it.