In Switzerland we have mail-in voting since many years and it is the most used voting option. The way it works to ensure that votes aren't fraudulent / duplicate votes while providing voter privacy is as follows: Inside the main envelope there is your transmission card ("Stimmrechtsausweis") which is signed by you and a separate anonymous return envelope with your actual votes. When it arrives in the municipality the transmission card will be verrified and (if valid) the still closed return envelope will be put into the ballot for later counting.

See https://en.m.wikipedia.org/wiki/Voting_in_Switzerland for more information.