What is the difference between removing a startup-application and un-checking it?
In this example, what is the difference between leaving "Snap user application autostart helper" unchecked verses clicking "Remove"?
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~/.config/autostart/(.desktop file) is deleted.
If you uncheck it, its line in the .desktop file:
is changed into:
The original of the .desktop file in your example resides in
/etc/xdg/autostart, which is the "global" directory for autostart applications. These work for all users.
If you uncheck one of these, a local copy is made, with the changes I described.
The local, "unchecked" one will then overrule the one in