[2020] Connected to Steam - Lost Characters and Stash

The game doesn’t delete saves on uninstall. The game files are actually identical on steam or stand alone. What I think happened is that the steam cloud saves kicked in at a very unfortunate time and overwrote the saves with blank ones. I could be wrong and it should ask you first.

Your saves are located in:
C:\Users\[username]\AppData\LocalLow\Eleventh Hour Games\Last Epoch\Saves

If those files were modified in the last day, then yea it was probably overwritten.