I guess the subject tells for itself
Does anyone know which files are used to save current checkpoint for different player profiles. I supposed that copying old .sav files into "savegames" folder will be enough, but it seems that there is some other file where Far Cry store additional data.

I had to uninstall Far Cry half way through to end. I copied Profiles directory to different place on HD in order to back it up later. After few days when I installed the fresh copy, I tried to copy those old save files (i.e. Profiles directory) over existent (new and empty) ones. Nothing happens - old save files are invisible.
Tried to make new Profile and played 5 checkpoints into game, then tried to replace those save files (only .sav files) with my old ones. Eventhough they have same name, none was visible!
I made new Profile and played 5 checkpoints again. Then I deleted last one (No. 5) and restarted the game. Game reported that checkpoint 4 is last saved game. I am bit confused at this stage. I only concluded that Far Cry somewhere saves the current level, and will not except other save files without altering some .cfg files, but I could not find which. Another possibility is that Far Cry looks most current date (because it is not name related).

Any ideas what to do?

Tough one, huh? No answer?

But I solved it

It was version issue. Old save files were from Far Cry updated to ver. 1.4, and I was trying to load them into official ver. 1.0. Updated to ver 1.4 and voila it works. Just copy / paste save files into Profiles folder and it works like a charm.

Bottom line: Far Cry ver.1.0 and ver.1.4 make uncompatibile save files.