I think i have the same issue:
I have an SSD with enough space, so i changed the ETS2 steam files to this path (D:)----> ok!
Then i moved all the users files (profile, mods and others) to D: path (the entire mydocuments/ets2 directory)
I applied changes to the launch parameters using the -homedir code (where the users files are, same path but different directory with the steam files)
And when i run the profile in the game, there is no mods on the list
How do you fix that problem??