I always make a backup, too.  I usually rebuild the sort files only.

If I run into an error during the data conversion, I go back and rebuild the file that's causing the problem.

I usually don't rebuild anything before upgrading unless a problem appears. I know a few resellers who do rebuild the files. 

I tend to take the approach to just run an initial test upgrade and see what issues may appear. This has worked well for almost every upgrade. The exceptions are those where you know going in that there is a likelihood of damage.

And, yes, it would be nice to have a one-click rebuild option especially if that could be scheduled for after-hours.

I rebuild key files when upgrading from really old versions, and if I know the customer has encountered errors / network connectivity issues (with high-likelihood of file corruption).  For everything except Premium I migrate from a folder copy of MAS90.  Premium doesn't need rebuild key files at all.

Even the ability to chain the modules together for multiple RKF running in sequence would help (...less monotonous baby-sitting of blue bars creeping across the screen).  I know if the utility crashes, the log file to that point in time is lost... so fixing that would be nice too.