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I know, I know this is an old question, but none of the threads about this issue ever result in a solution.

I only just started playing and was a couple of centuries in and had set my autosave to monthly (not knowing the looming save issue) and had made one save manually early on. Then after hours of real time play I stopped for the night and tried to do a manual save. I got the error "too many saved games in this session". So, I began deleting the 100+ monthly auto saves but they were still there. I followed many threads in this forum and elsewhere which mostly focused on deleting the saves in my docs and also the index file. Nothing I do allows me to save anything. I've seen threads going back to 2017 about this issue, so 5 years later and still no fix?

All I can say is that I'm glad I got this game for free through Prime Gaming as paying for this level of incompetence would be crazy.
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i have never had Stellaris say I have too many save games but I also play ironman with autosaves set to min

if you play iron man then your saves go into the pops_filestorage folder and if you don't then they just go into saves... as both folders default to documents and Microsoft loves putting documents into OneDrive I'm assuming you have a sync issue
I get this a lot, because I'm a big savescummer and save often. But I don't have trouble fixing it.

In-game, under settings->Gameplay, I have Autosave set to Monthly. This causes the game to save every month, but it only creates 5 save files, as it erases the oldest one when making a new one. The name of these files is of the form autosave_2401.10.01.sav, where 2401 is the game year and 10.01 is the date.

Second, I have 'cloud save' in that same set of settings set to Off. That's very important.

Given I'm not playing ironman, and have cloud saving off, my saves are going to a subdir under my documents directory (win 10).

<documents>\Paradox Interactive\Stellaris\save games\lostleague5_228210959\ is the directory.

I get a new and different directory under save games for each game I start. The current game is lost league 5, and the game invents that random number.

Just to be certain, I've deleted every other directory under "save games".

I have another directory that I made myself, at
<documents>\Paradox Interactive\Stellaris\other save games\lostleague5\. When I get the message, I go into the first direction using the file explorer, select all (ctrl-A), cut (ctrl-X) and navigate up two levels and down into the other directory and paste them (ctrl-P). They if I go back to the first directory the files *are no longer there*.

Then, when in game I do the 'save menu', (escape, save game), the dialog that lets you name the save shows *no other saves*. That's important. If it is showing other saves, then you haven't deleted the right files.

If you are doing all of this correctly, and are still seeing the old saves when you try to save, then I think something is going on that the game is not getting an updated read of your save directory properly. You can try to go into the 'load game' menu instead, and then escape back out of it, and that might force a re-read of that folder.

Beyond that, my only advice is to play until the game saves automatically at the end of the month and then quit.

I suspect from what you've written that somehow the place the game is saving is not the same place you have been trying to delete files from, and that once you clear out the actual location you'll be fine. It all works fine for me...

If nothing else works, you could try changing cloud saves to 'yes' and see if you can save on the cloud so that you can at least quit the game.

After you get out of the game, reboot (in case the problem is that files are being left open that should be closed - open files can't be deleted in windows. Then move all your saves but the most recent to another location and then launch the game and see if that makes it any better.

Good luck.
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ussnorway: i have never had Stellaris say I have too many save games but I also play ironman with autosaves set to min

if you play iron man then your saves go into the pops_filestorage folder and if you don't then they just go into saves... as both folders default to documents and Microsoft loves putting documents into OneDrive I'm assuming you have a sync issue
I'm not going to play ironman just in case I click something wrong, like accidentally set my main planet to purge, or save file gets corrupted.

Ironman isn't the solution.
you can make backups of the ironman saves so that avoids pilot errors like that... anyway play however you like mate