To reproduce:
1. Open attached project in 5.4
2. Notice that line 107 of the script RPGController.cs creates an object of type NavMeshAgent called NavMeshAgent
3. Notice that lines 629 and 630 refer to this object like this:

if (NavMeshAgent.remainingDistance <= NavMeshAgent.radius + 0.1F ||

(!NavMeshAgent.pathPending && NavMeshAgent.remainingDistance <= NavMeshAgent.stoppingDistance &&

(!NavMeshAgent.hasPath || NavMeshAgent.velocity.sqrMagnitude == 0f)))

4. Open the attached project in 5.5, and let the script updater do its work
5. Notice that lines 629 and 630 get changed to this:

if (NavMeshAgent.remainingDistance <= NavMeshAgent.radius + 0.1F ||

(!NavMeshAgent.pathPending && NavMeshAgent.remainingDistance <= NavMeshAgent.stoppingDistance &&

(!NavMeshAgent.hasPath || UnityEngine.AI.NavMeshAgent.velocity.sqrMagnitude == 0f)))

The important part here is that NavMeshAgent.velocity.sqrMagnitude (an object) gets changed to UnityEngine.AI.NavMeshAgent.velocity.sqrMagnitude (a static class), producing incorrect results and compilation errors.