Since the update from 04.04.18 the game moved to ScummVM. To make your old save files compatible, you will have to rename and move them to game's installation folder, default path is:
C:\GOG Games\Myst Masterpiece Edition\
C:\Program Files (x86)\Galaxy\Games\Myst Masterpiece Edition\
Save files should use the following naming scheme: myst-000.mys, myst-001.mys, myst-002.mys, etc.