From an in-universe perspective, the best answer is "morphing is just like that sometimes". There are numerous cases where morphing technology is shown contradicting what the Animorphs are told about it, usually in small ways. Of course, in some of those cases, the real-world answer is that K.A. Applegate and/or her ghostwriters made mistakes, miscommunicated, or just came up with better ideas after the fact. However, it appears that some of this ambiguity is in-universe as well.
Morphing is a relatively new technology, probably about an Andalite generation old, or maybe less. (Full, spoiler-y discussion of this point can be found in this answer.) Andalites consider morphing itself more of an art than a science, even to the point of having staged performances. Prodigies at morphing can push the limits of what's usually considered possible.
Without getting into too many details, there are both situations where morphing repairs damage like you're suggesting it would, and situations where it doesn't. I suspect there will never be a definitive in-universe answer about why.