Hi people.
From what I understand the problem lies on being unable to sync the achievements with GOG Galaxy, after unlocking them in-game, because at some point you needed to delete the galaxy.dll in order to run the game.
Did you ever unlock any other achievements and if yes did you sync them and how, or is it that you want to sync only those two specific achievements?
At any rate I suggest to first uninstall and reinstall the GOG Galaxy client.
Then to install the game using the offline backup installers and finally to import the installation to the GOG Galaxy client.
Might be helpful to let us know the version of your OS and the downloaded game you are running.
Let me know how that goes.
Cheers.