Classified information has to be kept in an approved storage container, and Top Secret information requires two person integrity, so two people have to open a safe and document the opening and closing. Inventory is done every time a safe is opened and closed, and anything removed is noted. This is not based on someone's administration, unless an administration completely changes the record keeping process, which would require publication of the new directives. I can tell you that has not happened. Combinations are required to be changed every time personnel change so that people who no longer require access do not have the combination. This is also recorded. All of the above is the same for a SCIF that is opened or closed, and those usually have safes in them as well. All of the documentation must be maintained/kept for a set period of time so that audits can be done. Programs are audited routinely to make sure that things are kept running properly.
Is it always perfect? No, people are people, and people make mistakes. But mistakes are usually noted and corrected rather quickly when it comes to things like this.