It's bloody dangerous tweaking file timestamps, and it's even more dangerous to assume, as you're doing here, that a timestamp means something other than what it ordinarily means. With anything, not just timestamps, doing that hurts reliability and maintainability, it makes comprehension and auditing difficult. The files changed for a legitimate reason, and your system broke.
The timestamps you want to check are recorded in commit metadata, and getting to them isn't efficient enough. Switch to extracting the timestamps to an index file or some such and check them there. Otherwise you're reduced to telling people learning your setup that "not everything is what it seems to be".