In order to speed up the starting time for GalCiv3, it doesn't read and compile the xml files that contain all the data. Instead it reads precompiled files with all the data. There are several of these. In a post some time in the past one of the devs added a comment that they are usually updated if they are more than a certain amount of time old, if I remember correctly. I don't remember what the time was. I also don't know if it was here or on Steam, and I haven't been able to find it.
After validating the files, I have checked which files were updated by searching for files that were changed "today" and sorting by time to get all the ones changed "now" together in the listing. They all have an extension of either .bin or .dat. I usually get 4 to 6 files that are updated.
It's not a sign of a problem, and it's nothing to worry about if these are the files that are being updated.