The rep scheme (i.e. the number of sets and reps) will change if the minimum number of reps needed to progress are not achieved on your AMRAP set. The GZCLP v4.1 spreadsheet by /u/blacknoir will automatically account for this as long you input the number of reps achieved.
For example, if the necessary reps are not achieved using the 5x3 (5 sets of 3 reps), then you will move to the 6x2 rep scheme at the same weight.