If I understand you correctly and my understanding of OMM is correct, then no, OMM does not rewrite files at each launch, it does it once and never checks again. So if an update overwrites the files OMM does not know or care.
If look in your DCS folder after an update without uninstalling the mods you will see a /backup folder with all the files it overwrote.
Please bear in mind that for the last 400 years I have uninstalled mods every time an update comes through, so I am not entirely sure how dcs behaves anymore with regards to alien files as things may have changed, but that's how it used to be back in the bronze age.