Yup.
Probably it's not recommended but I've never had an error from upgrading that way.
Here are the steps I take:
1. Back up the board (we routinely do this anyway).
2. Close the board down in CP.
3. Go to the Upgrade page.
4. Upload all of the default (required) files that come with an upgrade onto the server.
5. Upload all of the files that I've edited (replacing the default files in #2).
6. Check to make sure all required files were uploaded correctly.
7. Hope for the best.
8. Click the "Upgrade" button.
9. Open the board and wait for the reaction by the members.
Anyway, I hope it works for you. If it doesn't then just redo the upgrade the way you normally have in the past.
