Are you using the same computer? Different computers? In either case:

Disable Steam Cloud saving for Valheim for all Steam profiles on a computer, otherwise it will happily overwrite all data whenever a different person Steam account logs on the computer because the data is per windows profile.
Steam Cloud also has sinc issues across many many games.
It's one of the many many issues with Steam Cloud. Steam doesn't really address it because people get upset with whatever game its effecting despite being a problem with Steam, not the games.