I've been looking for that... there is a "SaveData.map" file which holds the waypoints, so next time you lose the waypoints, see if that file is still in your Save folder, and a valid text document - "X:\Users\ UserName\ Documents\ SH4SaveFolder\ data\ cfg\ SaveGames\ xxxxxxxx\ SaveData.map", where "X" = drive letter and "x" = numbers in folder name.
I have not found a date and / or time holder yet, but I have not searched very deeply in the binary files. I don't understand why a Load Save would not bring in all of the files. Maybe the "SaveData.map" is just a "back-up" of the true data that's in a binary file instead... ?? I sure do wish aanker would get well and re-join us. He knows a lot about the save folders.