download and unzip the updated file next to the old one, copy your old saved game from this path (Z:\...\Agent17-0.24\game\saves) onto the new one, as in copy the whole file "saves" rather than its content.
Launch the new version (should have 0.25.9 in the name) and check if you can access your old saves; if yes, delete the version 0.24 of the game. If not start the process over, version 0.24 and its save should still be there.
There is sadly no update like what steam would do. You need to install V0.25 fresh, move your save manually from v0.24 and then delete the v0.24 entirely.