Hello everyone and anyone who happens to stumble across this topic. I am having problems with saving progress for this game! My save is being reset to 0% Story Not Started!! Everytime I close and then relaunch the game it gives me a save with 0%. I'm assuming this is the save file found in Documents/WB Games/Batman Arkham Origins/SaveData.

Running on Windows 10.

Here's what I've done:

Added the Batman Arkham Origins directory folder to Windows Virus & Threat Protection exclusions
Added the Batman Arkham Origins exe to Windows Virus & Threat Protection exclusions
Added the WBGames folder to Windows Virus & Threat Protection exclusions

Running BatmanOrigins as an Administrator
Changing the compatibility options of the exe to always run as administrator for all users

This has been unsuccessful so far.
Weirdly enough it saved earlier today, and I was able to continue my progress after relaunching the game. It has suddenly reverted back to not working. My game graphics settings were saved yesterday after changing them.

Are there any other potential fixes I should try? Perhaps a mod for manual saves?

I hate Windows.

Here's an update 1 hour later, I believe I found the cause of the problem, read the tldr at the bottom if you're encountering a similar problem. I'm leaving this topic open as it may help people in the future.

I realised I was missing a few notes that are important for clarification.
I have only ever launched the game using the shortcut and not the play button from GOG Galaxy.
I had installed a mod that replaces the button icons with PS4 ones. For this mod to work, it requires replacing the exe with a modded one that's provided in the mod pack.

After my previous post, I carried out a few more steps.

1. I reverified and repaired the files via GOG (this of course deleted my mods).
2. Checked for any pending updates via GOG.
3. Relaunched the game and started a new save file. It was at this point when I saw the "Saving" icon appear, and it appears very often.

I had not seen in my previous lost save at any point the Saving icon, which leads me to believe the autosaving feature was broken. After testing the save, closing and relaunching the game with and without the mod I discovered the glitch that caused me to lose about 5 hours of progress.

Glitch Description:
Upon launching the game, you are brought to the initial launch screen where you are asked to click a button to start, you are then presented with your 4 save slots. If you back out of this, you may see a black screen and then it appears as if you return to the initial launch screen. However you are now actually in a GLITCHED STATE, and clicking to start skips the save slot selection screen and then brings up options such as Story, the DLC, Options, Extras etc... If you then hit story, it only presents you with New Game, New Game + etc.. There is no option to continue your saved game if you had one already. If you hit New Game to play the game, you will not be able to save your game, autosave will not work!!

This was my mistake, I had triggered the glitch when booting up for the first time and started a new game, not knowing what the autosave would look like. Through my 5 hour run, the autosave never worked and closing the game lost all my progress. I'm not sure how I was able to continue my progress in that cursed playthrough, I may have misremembered actually closing the game and instead I must have simply gone back to the main menu.

The autosave may not work during one of these glitched runs, as you never actually select a save slot so the game may not know where to autosave. This is just theorising though.


TLDR;
Arkham Origins has a glitch where if you launch the game, and press O/B (whatever button depending on your controller) to back out of the save slot selection screen, you have entered a glitched main manu where you are only given the option to start a New Game. DO NOT START THE GAME HERE AS YOUR RUN WILL NOT AUTOSAVE. Exit out of the game fully, and relaunch and your saved game should still be there, if you have already started. DO NOT BACK OUT OF THE SAVE SELECTION SCREEN, YOU WILL ENTER A GLITCHED MAIN MENU. IF YOU DO, RELAUNCH THE GAME.

Other steps to ensure the game will autosave:
1. Reverify game files and check for pending updates (easiest to do if you dont have mods, must reinstall them after this step.)
2. Run the game as administrator. Right click the exe file, go to Properties, then the Compatibiity tab, and check the "Run this program as an administrator" box. Do this for all users if you wish.
3. Under Windows Security, Virus & Threat Protection, Ransomware protection; turn off Controlled Folder Access or click "Allow an app through controlled folder access" and add the game's exe file.
4. Go to Virus & Threat Protection, manage settings and then Add or Remove exclusions. Here you want to add as exclusions: the Documents/WB Games folder, the Batman Arkham Origins directory folder, and the game's exe file.

sorry for long post but i wanted to put this here in case people in the future have problems, no doubt WBGames will never fix this.