I’m running an iMac on OSX 12.12 Sierra with Cubase 9 and I’ve never seen an instance where I re-export the same mixdown (which by default will give you a prompt that it will perform an overwrite in the file exists) and have had any issues whatsoever with the wrong file size, noted issues on playback in itunes or anything of the like.
And since a file overwrite isn’t a complex or proprietary task and is a standard process irrelevant of the OS or software; I’m going to suggest your issue is very likely specific to the version of the OS, your system or possibly both.
While I totally get the rationale of keeping an older OS (2 years in your case); sometimes it makes sense to upgrade when and if you seen anomalies that no one else is reporting running on later OS versions.
Could also be your hardware or some internal file system corruption. Hard to say really.
If you want to continue using El Capitan for whatever reason, my advice would be to see if the issue is reproducible on another system running the same OS (if possible) or minimally install a VM like VMWare Fusion or one of the other free VM’s available like Virtual Box with El Capitan and Cubase and see if the results are consistent.