I’ll start off with a disclaimer: even after we looked at the data for the project, we can’t say for certain what happened. Paratext is pretty strict about allowing the wrong user to change a file so the likely situation is that the files were changed outside of Paratext. However, even with that, it wouldn’t explain why the changes were not showing up in Verse History.
We did some digging and all of the changes by Tuomas (I’m assuming the person in question) all seem to be duplicates of changes that other people have made. The changes in GAL are identical to changes made by Helena on Feb. 2, 2016. The changes in 2CO are identical to changes made by Helge on Feb. 4, 2016. Our only guess of how this could happen is that Tuomas somehow got copies of the files and replaced them on his/her machine without going through a Send/Receive.
This also explains why the changes are not showing up in Verse History as we filter out versions that are textually identical to the previous version (i.e. in the history flow, the text did not actually change).