Despite using steam cloud saves, F.E.A.R 3 checks your save against your windows user account, and if the one in the save and the real one don't match, erases your save files. I suspect this is to prevent people sharing saves, but this means Steam Cloud Saves are effectively useless, unless used on the exact same windows install as the original.

This is annoying for speedruns, as level ups enable slow motion, losing time. the only way to avoid this is to already be level 21, which takes about 5 runs depending on your play style and which character you play.

You can still import a save file from another computer, but this requires some shenanigans:

1. open F.E.A.R 3 and start the first level. after the cutscene where Point Man picks up the earpiece, wait for the "Saving" text in the top right to disappear, then close the game.
2. Locate your donor save file named User.profile(that you have downloaded, level 21) and your patient save file (that is the actual save, in c:/Program Files/Steam/userdata/[your steamID]/21100/local on windows, or $HOME/.local/share/Steam/userdata/[your steamID]/21100/local on linux).
3. Copy the bytes 64 to 564 from the donor save, and overwrite the same bytes in the partient save. On windows, you can use a hex editor (http://www.chmaas.handshake.de/) to do this. on Linux, you can use dd: dd if=[path to donor save] of=[path to patient save] bs=1 count=501 skip=63 seek=63 conv=notrunc
4. That should be it. launch F.E.A.R 3 again and you should be level 21 in the menu, the level icon next to your name displaying a golden Biohazard symbol.