Only had one working save that was at turn 70. When I went in it I knew I realized it's an old save and I'm actually further ahead. I went into save folder and there is the autosave of that game at turn 98, but it's in TMP format instead of SAV, which makes it unloadable. Running steam and/or Endless Space 2 as admin does not fix it. Windows 10 x64, latest official version of game, not using G2G mod.

Hmm, this was an issue that was thought to be fixed in 1.0.36, 

It seems Bug Fixing is a game of whack-a-mole that you can't win.

All you need to do is rename the file from [savename].tmp to [savename].sav or [savename].zip and then the game should be able to load it.

The Common cause of the issue before was antiviruses, What antivirus are you using? 

Could you upload your diagnostics file, it can be found in;

"%My Documents%\Endless Space 2\Temporary Files"

there should be up to 10 "Diagnostics - Date @Time.html" files with the date & time of when the game launched 

could you upload the one from when the autosave was made?

(If the file is larger then 4MB put it in a zip before uploading it)

Also if you can't load the renamed file could you upload it?

ES2 Diagnostic.rar

Diagnostics file you asked for that was created one minute after the autosave was made.

Renamed "AutoSave 98.sav.72.tmp" to "AutoSave 98.sav". Game was loadable, but star lanes connecting systems belonging to the same constellation, that were once discovered, have dissapeared.

Sounds like it did not save correctly could you upload that autosave?

From the Diagnostics:

JobScheduler raised an exception: System.IO.FileNotFoundException.

JobSchedulerManager:JobScheduler_ExceptionRaised(System.Reflection.ParameterInfo, System.Reflection.ParameterInfo) Amplitude.AI.Common.Threading.JobScheduler:WorkerThreadRun(System.Reflection.ParameterInfo)

C:\Users\casua\OneDrive\Documents\Endless Space 2\Save Files\AutoSave 98.sav.72.tmp.161.tmp does not exist

System.IO.File:Move(System.Reflection.ParameterInfo, System.Reflection.ParameterInfo) ICSharpCode.SharpZipLib.Zip.DiskArchiveStorage:ConvertTemporaryToFinal() ICSharpCode.SharpZipLib.Zip.ZipFile:RunUpdates() ICSharpCode.SharpZipLib.Zip.ZipFile:CommitUpdate() Amplitude.IO.Archive:Add(System.Reflection.ParameterInfo, System.Reflection.ParameterInfo, System.Reflection.ParameterInfo) ArchiveJob:Run() Amplitude.AI.Common.Threading.JobScheduler:WorkerThreadRun(System.Reflection.ParameterInfo)

Not sure what is going on with the "AutoSave 98.sav.72.tmp.161.tmp" but it may be the cause.

AutoSave 98.sav

The save only contains Galaxy.bin, Game.bin & GameSaveDescriptor.bin (You can open it as a zip)

It's missing the AI Folder, The Fog of War Folder (this is why your discovered area has been reset)

GameStatistics.bin & Prism.bin.

I'm honestly surprised that the game loaded from that save.

It seems something when wrong while it was saving and it did not fully save everything.

Hopefully the devs will be able to get to the bottom of this with the help of the files you have provided,

I would expect a dev may give a response on Monday.

Okay, thanks for your help.

Thanks for your report Zaughtilo and for your help CyRob!

As CyRob said, the save file has been corrupted during the saving processes. Could you tell me which antivirus do you use? 

Webroot SecureAnywhere