Joplin stores some if its user-related data in the path "%userprofile%/.config/joplin-desktop". This creates a ".config" directory in the user's profile directory, which looks confusing because it is not where you should store user-related app data on Windows. The correct path for that is "%localappdata% or "%appdata%, depending on the type of content.
Judging from what I found in that directory, it seems to be user-related data that is intended stay on the machine: log files, databases, tmp and resources under control of Joplin's sync mechanism.
All of this should reside %localappdata%. Also, %temp% directory is recommended for temporary user data.
For more details: https://www.advancedinstaller.com/appdata-localappdata-programdata.html