I have posted here before about what works for me, so with sympathy for the OP, here goes:
(1) Exclude the save path of the game <Documents>Egosoft>[AP or TC]>Save, as well as the Steam path <c>Program files x86>Steam>
from your AV and Anti-Malware apps
(2) When you save and quit from the Ego load window, go to either the the Task Tray (in the Right Hand Corner) or the Steam App (if it is open) and hit Exit. Thils will force Steam to flush and close the Steam Cloud handle. I noticed that most of my lost DID save game are the result of exiting Steam in a haste (Honey-do calls, which I can't miss or else risk a divorce

)
Other safeguard include:
(3) Have a UPS for your comp, and put both the comp and the router on it.
(4) If you are running Windows 7, disable reboot-on-update. I posted the procedure somewhere in this forum before. Windows 7 may decide to reboot your computer after it has applied a Windows Update, despite the fact that you have a program running in the foreground. The guy at Microsoft that did that codes ought to be shot!!!!!!