Your problem is too wide to narrow down, so I'll list down what may be a problem.
- Book 1 saves cant be loaded to book 2 and vice versa
-Is the "saves" folder inside the game folder.. Like so - "MTWYBook2Chapter18-0.18-pc\game\saves"
- Did you copy the persistent save file to your flash drive? it's a file that says "persistent" inside the saves folder.
-Lastly, the game actually makes a separate save in this location C:\Users\"Username"\AppData\Roaming\RenPy\Mytimewithyou-1616056931. You don't even have to save your save file in a flash drive. So unless you deleted the save file in this location, even if you uninstall our game many times, your saves would remain.