Blender autosave files shouldn't be saved to the user's /run folder as it's very restricted with regards to available space. Once it's filled other programs are likely to fail to start.
❯ du -sh /run/user/1000/.flatpak/org.blender.Blender/*
1.4G /run/user/1000/.flatpak/org.blender.Blender/tmp
0 /run/user/1000/.flatpak/org.blender.Blender/xdg-run
Blender autosave files shouldn't be saved to the user's /run folder as it's very restricted with regards to available space. Once it's filled other programs are likely to fail to start.