Each update to the CodeMatrix database increments an internal counter, known as the change reference number. CodeMatrix offers the facility to identify file revisions using this number, so it may be used to view snapshots of the database at any point in time. A common use for this facility is to recreate a set of source files used in a particular software build when subsequent changes have been made to these files.

Change reference numbers are similar to labels, but with the advantage that no specific action is required to record the state, and any historic system state may be restored, not just those explicitly labelled. Labels on the other hand are useful when file revisions from multiple changes need to be identified.

CodeMatrix allows multiple updates to be grouped into a transaction, in which case a single change reference number will represent the system state at the end of the transaction.