I’ve observed interesting issue, we have an option “Push sources” in GitHub integration but sometimes it still brings GitHub version of file into Crowdin, even though I’ve changed it in Crowdin.
We have synch schedule once per 12 hours and sometimes use Synch now option to get updates instantly.
Must say this bug appeared maybe 3-4 times, can’t say why it’s happening not regularly.
If you click “Synch now”, it will instantly read the sources from GitHub, update the files in Crowdin and the edits you have made will be overwritten, as you say, it will bring GitHub version of the file.
This is 100% the reason. That’s why you can’t track it, because it happens after manager clicked the button 
Just reduce synch schedule to 1 hour, it doesn’t affect performance at all and is fine for keeping things updated.