The entire point of a backup is to overwrite and replace bad data, though. If a backup was kept, it would logically follow that it would be possible to overwrite the damaged parts of the pattern, since we know that transports can succeed even if a portion if the pattern is lost.

Geordi specigically brings up it being impossible to materialise Franklin because his pattern had degraded too much, not that it was degraded at all, and would suggest that there's a threshold before repairs are no longer possible.

A transporter trace might not have existed to begin with, and depending on how the disease acted, any old traces might have been lost.

For example, if she had an illness that only started presenting itself long after she caught it, like Tholian shingles. There may no longer be a healthy trace to pull from, or the disease caused damage that a backup cannot sufficiently repair.

We do know that some health conditions generally preclude transport. It's not very healthy for foetuses to be transported. Voyager did it, and the baby had to spend several days in ICU to make sure that being transported didn't mangle their neurochemistry, which would suggest that's also something a transporter cannot readily fix.

As previously stated, I'm leaving NuTrek out of this discussion entirely as NuTrek doesn't care about continuity in the slightest.