DataGraph uses the Auto Save and Versioning features in the macOS. The AutoSave has a lot of benefits but it means that anytime a change is made, a version of file is saved. You simply can’t open a file without the change being registered. Here is a link to article I liked, that describes this feature (maybe in more detail that you are interested in!):
AUTO SAVE AND VERSIONS: AN OFTEN OVERLOOKED MAC FEATURE
The message you are seeing is generated from the macOS and is not something that DataGraph has control over. But it can occur in two ways we are aware of, either due to a synching protocol from something like dropbox, where they save a file in the DataGraph package, or in the instance that you are having, where you revert back to a prior version.
To save the file back to the version from when you opened:
1 – Select Revert the first time
2 – Then select Save Anyway when it pops up again
To have more control over what version you revert back to you can try using the Revert menu.
After reverting to a prior version, the system will still pop-up this message. Click ‘Save Anyway’ to continue. In this case, this message is something we need to check into further, to see if we can indicate to the system that the file is OK to save, but you do not have to make a new version of the file.