This screen recording show that on your work computer, those files were not present. Obsidian thought that this version of the vault was more up date and delete the files in the remote vault.
I am no conviced that this is a problem with obsidian or the leftover mess by the plugin you are using or your complicated setup (veracrypt and so on).
So my advice is to start fresh.
- delete your current remove vault.
- set up a computer with the files the way you want them.
- Create a remote vault and fully sync it.
- Create a new vault in your work computer, connect it to the remote vault and let it sync.
Don’t use that plugin for a while.
If it happens again, post open a new bug report.