I'm sorry you got hit by this. What you describe sounds similar to a bug that was fixed in the most recent update, v0.24, which released on Steam on Dec 20 and EGS on Dec 22. If this happened before those dates or if your version of the game didn't automatically update (you can check this by looking at the bottom right corner of the screen on the start menu when the game is first launched), it may be that an update will fix the problem.
If not, maybe there is another way to trigger the bug that the previous fix missed, in which case I will do my best to fix it as soon as possible. In this case, the next time you save and the game doesn't create a .dat file, could you send me the file C:\Users\[YOUR_USER_NAME]\AppData\LocalLow\Tom Johnson\Ecosystem\output_log.txt? It would need to be immediately after the bug - ie the game has not been launched since the failure to save occurred - but it would be a huge help for me to track down what's going wrong. If you have trouble attaching or pasting the file here on the forum, you can also email it to me at tom [at] ecosystem-game.com. Apologies again about the bug.