Follow engineering best practices. One thing you should never do is to write a new system, requiring it to perfectly emulate an old one. It can never work and there will always be unexpected deviations in system behavior. I.e. in Boeing's case it isn't so much about any particular flaws (faulty AoA sensor etc), it is about the whole idea of having a completely new aircraft design appearing to the pilot as if it was an old one. It is similar to replacing an Active Directory deployment with OpenLDAP and betting on users not noticing.
Another engineering best practice is to keep proper logs. The Toyota recalls from 2009 to 2011 were likely caused by some bugs but they weren't able to find the root cause. Ostensibly because not enough data were being logged.